1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 27b3     August 15, 2000   
       Copyright(c) 1984,1992  President and Fellows of Harvard College
                              All Rights Reserved
                     Current operating system: GNU LINUX
                 Created on  6/15/ 6 at 14:53:25 by user: fajer       

            Maximum number of ATOMS:     60120, and RESidues:       32000
            Current HEAP size:        10240000, and STACK size:    900000

 Processing passed argument "seed=928338"
 Parameter: SEED <- "928338"
 Processing passed argument "probe=CMTS"
 Parameter: PROBE <- "CMTS"
 Processing passed argument "spinlabel=mtsl"
 Parameter: SPINLABEL <- "MTSL"
 Processing passed argument "labelsegid=1"
 Parameter: LABELSEGID <- "1"
 Processing passed argument "labresid=64"
 Parameter: LABRESID <- "64"
 Processing passed argument "labresno=59"
 Parameter: LABRESNO <- "59"
 RDTITL> *...
 RDTITL> 
  
 CHARMM>     
  
 CHARMM>    BOMBLEVEL -2
  
 CHARMM>    WRNLEV 5
  
 CHARMM>    PRNLEV 5
  
 CHARMM>     
  
 CHARMM>    !Read the string file rtfprm.str to read topology and parameter files
 CHARMM>    OPEN READ UNIT 18 CARD NAME $SL_MOD/charmm/charmm_str/rtfprm.str
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_str/rtfprm.str::
 OPNLGU> Unit 18 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_str/rtfprm.str
  
 CHARMM>    STREAM UNIT 18

                    INPUT STREAM SWITCHING TO UNIT    18
 RDTITL> * STREAM FILE FOR READING RTF AND PRM FILES
 RDTITL> * NEEDED FOR ALL INP FILES
 RDTITL> * BY KS, 5/19/00, PF 7/21/02, 8/05
 RDTITL> *
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file (ASCII) and parameter file (ASCII) for protein
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_toph19.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_toph19.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_toph19.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> *
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read MSI support topology file for CHARMm19
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_charmm19_support.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_charmm19_support.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_charmm19_support.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * MSI SUPPORT FILE:
 TITLE> * INCLUDES TITRATABLE RESIDUES IN THEIR NEUTRAL STATES.
 TITLE> * INCLUDES MODIFIED C-TERMINUS PATCH
 TITLE> *
 **** WARNING from RTFRDR **** The total charge of the residue, GLUH,  -0.5600000,
 does not equal the expected charge,   0.0000000.
          RESI LYSD    0.00000
 There were   1 warning(s) from RTFRDR.
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSMTSSL (CMTS)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cmtssl2.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cmtssl2.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cmtssl2.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-MTSSL SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 4/21/00 BY KS
 TITLE> *
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSIASL (CIAS)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cias.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cias.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cias.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-IASL SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED BY KS ON 3/30/00
 TITLE> *
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSMSL (CMSL)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cmsl.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cmsl.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cmsl.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-MSL SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 3/31/00 BY KS
 TITLE> *
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSInVSL (CINV)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cinvsl.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cinvsl.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cinvsl.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-INVSL SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 4/17/00 BY KS
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 {DEFINE CYS-INVSL SPIN LABEL}
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO2242 (CHOQ)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho2242.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho2242.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho2242.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO2242 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 8/18/01 BY KS
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 {DEFINE CYS-HO2242 SPIN LABEL}
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO1710 (CHOC)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho1710.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho1710.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho1710.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO1710 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 8/23/01 BY KS, SHENPING 12/16/03
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 {DEFINE CYS-HO1710 SPIN LABEL}
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO2114 (CHOF)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho2114.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho2114.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho2114.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO2114 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 3/21/02 BY KS
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 {DEFINE CYS-HO2114 SPIN LABEL}
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO3002 (CHOZ)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho3002.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho3002.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho3002.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO3002 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 3/21/02 BY KS
 TITLE> *
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 {DEFINE CYS-HO3002 SPIN LABEL}
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO2101 (CHOR)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho2101.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho2101.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho2101.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO2101 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 5/28/02 BY KS
 TITLE> *
 WARNING from DECODF -- Zero length string being converted to 0.
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CYSHO2601 (CHOP)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cho2601.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cho2601.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cho2601.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-HO2601 SPIN LABEL: KS VERSION 1
 TITLE> * MSI SUPPORT FILE: MODIFIED 8/08/02 BY KS
 TITLE> *
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for CIADEDANS (CIAD)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_ciaedans.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_ciaedans.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_ciaedans.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-IAEDANS
 TITLE> * MSI SUPPORT FILE: MODIFIED 2/14/03 BY PF BASED ON PYRENE BY KS
 TITLE> *
 WARNING from DECODF -- Zero length string being converted to 0.
 **** Warning ****  The following extraneous characters
 were found while command processing in RTF reader
 O10
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !Open and read an extended atom with explicit polar hydrogens (CHARMm19)
 CHARMM>    !topology file for Cpyrene (CPYR)
 CHARMM>    OPEN READ UNIT 21 CARD NAME $SL_MOD/charmm19/pf_cpyrene.rtf
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_cpyrene.rtf::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_cpyrene.rtf
  
 CHARMM>    READ RTF UNIT 21 CARD APPEND
 MAINIO> Residue topology file being read from unit  21.
 TITLE> * TOPOLOGY FILE FOR CYS-PYRENE
 TITLE> * MSI SUPPORT FILE: MODIFIED 11/04/02 BY KS
 TITLE> *
 WARNING from DECODF -- Zero length string being converted to 0.
  
 CHARMM>    CLOSE UNIT 21
 VCLOSE: Closing unit   21 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME $SL_MOD/charmm19/pf_param19.prm
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm19/pf_param19.prm::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm19/pf_param19.prm
  
 CHARMM>    READ PARA UNIT 20 CARD

          PARAMETER FILE BEING READ FROM UNIT 20
 TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 PARRDR> WARNING: ATOMS IN BOND SL   OSL   250.00000   1.57500 DONT EXIST
 PARRDR> WARNING: ATOMS IN ANGLE O2L  SL   OSL    85.00000  98.00000 DONT EXIST
 PARRDR> WARNING: ATOMS IN ANGLE CTL2 OSL  SL     15.00000 109.00000 DONT EXIST
 **** Warning ****  The following extraneous characters
 were found while command processing in PARRDR
 27.00   1.90
 PARRDR> WARNING: ATOMS IN ANGLE CTL3 OSL  SL     15.00000 109.00000 DONT EXIST
 **** Warning ****  The following extraneous characters
 were found while command processing in PARRDR
 27.00   1.90
 PARRDR> WARNING: ATOMS IN PHI HAL3 CTL3 OSL  SL      0.00000    3   0.00000 DONT EXIST
 PARRDR> WARNING: ATOMS IN PHI CTL2 OSL  SL   O2L     0.00000    3   0.00000 DONT EXIST
 PARRDR> WARNING: ATOMS IN PHI CTL3 OSL  SL   O2L     0.00000    3   0.00000 DONT EXIST
 PARRDR> NOTE: atom type "OC  " is removed from previous group
 PARRDR> NOTE: atom type "OT  " is removed from previous group
 PARRDR> NOTE: atom type "OH2 " is removed from previous group
 PARRDR> NOTE: atom type "NC3 " is removed from previous group
 PARRDR> NOTE: atom type "NN6 " is removed from previous group
 PARRDR> NOTE: atom type "NN5 " is removed from previous group
 PARRDR> NOTE: atom type "ON  " is removed from previous group
 PARRDR> NOTE: atom type "SL  " is removed from previous group
 PARRDR> WARNING: ATOM FOR NBOND OSL  DOESNT EXIST
 PARRDR> Error: Repeated ANGLE parameter (601450): S     CR1E  C   
 *** LEVEL  0 WARNING *** BOMLEV IS   -2
 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
  
 CHARMM>    CLOSE UNIT 20
 VCLOSE: Closing unit   20 with status "KEEP"
  
 CHARMM>     
  
 VCLOSE: Closing unit   18 with status "KEEP"

                    RETURNING TO INPUT STREAM     5
  
 CHARMM>    !Read the PSF, COORD and IC files
 CHARMM>    OPEN READ UNIT 20 FORM NAME build.psf
 VOPEN> Attempting to open::build.psf::
 OPNLGU> Unit 20 opened for READONLY access to build.psf
  
 CHARMM>    READ PSF CARD UNIT 20
 MAINIO> Protein structure file being read from unit  20.
 TITLE>  *PSF FOR PROTEINX-CMTSL AT
 TITLE>  *  DATE:     6/15/ 6     14:51:36      CREATED BY USER: fajer
 TITLE>  *
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =     1992
         Number of dihedrals     =      825   Number of impropers  =      596
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>    CLOSE UNIT 20
 VCLOSE: Closing unit   20 with status "KEEP"
  
 CHARMM>    OPEN READ UNIT 20 FORM NAME build.crd
 VOPEN> Attempting to open::build.crd::
 OPNLGU> Unit 20 opened for READONLY access to build.crd
  
 CHARMM>    READ COOR CARD UNIT 20
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> *1MMD INITIAL GENERATED COORDINATES
 TITLE> *HEAVY ATOM POSTIONS TAKEN FROM 1STN.PDB
 TITLE> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 TITLE> *  DATE:     6/15/ 6     14:52:58      CREATED BY USER: FAJER
 TITLE> *
  
 CHARMM>    CLOSE UNIT 20
 VCLOSE: Closing unit   20 with status "KEEP"
  
 CHARMM>    OPEN READ UNIT 20 FORM NAME build.ic
 VOPEN> Attempting to open::build.ic::
 OPNLGU> Unit 20 opened for READONLY access to build.ic
  
 CHARMM>    READ IC CARD UNIT 20
 INTERNAL COORDINATES READ FROM UNIT 20
 TITLE> *PSF FOR PROTEINX-CMTSL AT
 TITLE> *  DATE:     6/15/ 6     14:51:36      CREATED BY USER: FAJER
 TITLE> *
 TITLE>  *PSF FOR PROTEINX-CMTSL AT
 TITLE>  *  DATE:     6/15/ 6     14:51:36      CREATED BY USER: FAJER
 TITLE>  *
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
 *** IN MATOM *** '??  ' ATOM TYPE NOT FOUND FOR RESIDUE  -99
  
 CHARMM>    CLOSE UNIT 20
 VCLOSE: Closing unit   20 with status "KEEP"
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME  $SL_MOD/charmm/charmm_mmcm_str/setglobals_pf.str
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/setglobals_pf.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/setglobals_pf.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET strpath $SL_MOD/charmm/charmm_mmcm_str	! path to mmcm stream files
 Parameter: STRPATH <- "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
  
 CHARMM>    SET strucid ". "					! identifier used in coord file titles
 Parameter: STRUCID <- "". ""
  
 CHARMM>    SET frameout frames				! name of subdirectory for storing structures
 Parameter: FRAMEOUT <- "FRAMES"
  
 CHARMM>    SET numrotate 1					! number of torsion angles to perturb at each iteration
 Parameter: NUMROTATE <- "1"
  
 CHARMM>    ! The following variables are binaries for setting which bonds are allowed to be
 CHARMM>    ! randomized during the search (1 = allow, 0 = do not allow)
 CHARMM>    SET chi1change 1
 Parameter: CHI1CHANGE <- "1"
  
 CHARMM>    SET chi2change 1
 Parameter: CHI2CHANGE <- "1"
  
 CHARMM>    SET chi3change 1
 Parameter: CHI3CHANGE <- "1"
  
 CHARMM>    SET chi4change 1
 Parameter: CHI4CHANGE <- "1"
  
 CHARMM>    SET chi5change 1
 Parameter: CHI5CHANGE <- "1"
  
 CHARMM>    SET chi6change 1
 Parameter: CHI6CHANGE <- "1"
  
 CHARMM>    SET chi7change 1
 Parameter: CHI7CHANGE <- "1"
  
 CHARMM>    ! If a dihedral is not part of the search, then you may want to constrain it during minimization
 CHARMM>    ! this set of variables (chi#conb) is a binary (chi#conb = 1 then constrain, chi#conb = 0 then don't)
 CHARMM>    ! NOTE: if the dihedral is not part of the probe, then set to 0 (for example MTSSL has only
 CHARMM>    ! five bonds in its tether, so set 6 and 7 to 0.
 CHARMM>    SET chi1conb 0
 Parameter: CHI1CONB <- "0"
  
 CHARMM>    SET chi2conb 0
 Parameter: CHI2CONB <- "0"
  
 CHARMM>    SET chi3conb 0
 Parameter: CHI3CONB <- "0"
  
 CHARMM>    SET chi4conb 0
 Parameter: CHI4CONB <- "0"
  
 CHARMM>    SET chi5conb 0
 Parameter: CHI5CONB <- "0"
  
 CHARMM>    SET chi6conb 0
 Parameter: CHI6CONB <- "0"
  
 CHARMM>    SET chi7conb 0
 Parameter: CHI7CONB <- "0"
  
 CHARMM>    ! If a dihedral is to be constrained to be near a given value, then provide that value as chi#conv
 CHARMM>    ! also must provide the force constant as chi#conf
 CHARMM>    SET chi1conv   0.0
 Parameter: CHI1CONV <- "0.0"
  
 CHARMM>    SET chi2conv   0.0
 Parameter: CHI2CONV <- "0.0"
  
 CHARMM>    SET chi3conv   0.0
 Parameter: CHI3CONV <- "0.0"
  
 CHARMM>    SET chi4conv   0.0
 Parameter: CHI4CONV <- "0.0"
  
 CHARMM>    SET chi5conv   0.0
 Parameter: CHI5CONV <- "0.0"
  
 CHARMM>    SET chi6conv   0.0
 Parameter: CHI6CONV <- "0.0"
  
 CHARMM>    SET chi7conv   0.0
 Parameter: CHI7CONV <- "0.0"
  
 CHARMM>     
  
 CHARMM>    SET chi1conf  0.0
 Parameter: CHI1CONF <- "0.0"
  
 CHARMM>    SET chi2conf  0.0
 Parameter: CHI2CONF <- "0.0"
  
 CHARMM>    SET chi3conf  0.0
 Parameter: CHI3CONF <- "0.0"
  
 CHARMM>    SET chi4conf  0.0
 Parameter: CHI4CONF <- "0.0"
  
 CHARMM>    SET chi5conf  0.0
 Parameter: CHI5CONF <- "0.0"
  
 CHARMM>    SET chi6conf  0.0
 Parameter: CHI6CONF <- "0.0"
  
 CHARMM>    SET chi7conf  0.0
 Parameter: CHI7CONF <- "0.0"
  
 CHARMM>     
  
 CHARMM>    SET T  500					! temperature
 Parameter: T <- "500"
  
 CHARMM>     
  
 CHARMM>    ! Define the set of atoms allowed to move during minimizations.
 CHARMM>    ! All other atoms will be fixed in minimizaiton.str
 CHARMM>    ! Only energy among moving atoms and between moving and fixed sets
 CHARMM>    ! will be calculated and minimizaed.
 CHARMM>    ! Can use ALL as selection to allow all atoms to move.
 CHARMM>    ! below is the spin label and cysteine upto and inclusive C-alpha carbon.  Backbone of cysteine is fixed.
 CHARMM>    ! PF defines only a defined residue in multispin label file
 CHARMM>    DEFINE moveset1 SELE RESName @probe .AND. .NOT. ( RESName @probe .AND. ( TYPE CA .OR. TYPE N .OR. TYPE H .OR. TYPE C .OR. TYPE O )) END
 Parameter: PROBE -> "CMTS"
 Parameter: PROBE -> "CMTS"
 SELRPN>     14 atoms have been selected out of   1361
  
 CHARMM>    DEFINE moveset2 SELE RESID @labresid END
 Parameter: LABRESID -> "64"
 SELRPN>     19 atoms have been selected out of   1361
  
 CHARMM>    DEFINE moveset SELE moveset1 .AND. moveset2 END
 SELRPN>     14 atoms have been selected out of   1361
  
 CHARMM>     
  
 CHARMM>    ! Define the set of atoms whose coordinates will change by random changes in label torsion angles.
 CHARMM>    ! this is for the IC (internal coordinates) tables which rebuilds the spin lable after each rotation (don't worry
 CHARMM>    ! about non-spin moveset atoms as no IC tables are needed for them
 CHARMM>    ! This setup actually includes all the atoms whose coords would be altered by a rotation about the
 CHARMM>    ! bond most proximal to the backbone but elimnates the need for a bunch of if statements.
 CHARMM>    DEFINE spinset1 SELE RESName @probe .AND. .NOT. ( RESName @probe .AND. ( TYPE CA .OR. TYPE N .OR. TYPE H .OR. TYPE C .OR. TYPE O )) END
 Parameter: PROBE -> "CMTS"
 Parameter: PROBE -> "CMTS"
 SELRPN>     14 atoms have been selected out of   1361
  
 CHARMM>    DEFINE spinset2 SELE RESID @labresid END
 Parameter: LABRESID -> "64"
 SELRPN>     19 atoms have been selected out of   1361
  
 CHARMM>    DEFINE spinset SELE spinset1 .AND. spinset2 END
 SELRPN>     14 atoms have been selected out of   1361
  
 CHARMM>     
  
 CHARMM>    ! Set the atoms defining the torsion angles
 CHARMM>    ! read labels from strem file
 CHARMM>     
  
 CHARMM>    OPEN READ UNIT 18 CARD NAME @strpath/@spinlabel.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: SPINLABEL -> "MTSL"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mtsl.str::
 OPNLGU> Unit 18 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mtsl.str
  
 CHARMM>    ! execute commands in the opened file
 CHARMM>    STREAM UNIT 18

                    INPUT STREAM SWITCHING TO UNIT    18
 RDTITL> SET BONDS 5
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET bonds 5
 Parameter: BONDS <- "5"
  
 CHARMM>    SET chi1atom1 N
 Parameter: CHI1ATOM1 <- "N"
  
 CHARMM>    SET chi1atom2 CA
 Parameter: CHI1ATOM2 <- "CA"
  
 CHARMM>    SET chi1atom3 CB
 Parameter: CHI1ATOM3 <- "CB"
  
 CHARMM>    SET chi1atom4 SG
 Parameter: CHI1ATOM4 <- "SG"
  
 CHARMM>    SET chi2atom1 CA
 Parameter: CHI2ATOM1 <- "CA"
  
 CHARMM>    SET chi2atom2 CB
 Parameter: CHI2ATOM2 <- "CB"
  
 CHARMM>    SET chi2atom3 SG
 Parameter: CHI2ATOM3 <- "SG"
  
 CHARMM>    SET chi2atom4 S1
 Parameter: CHI2ATOM4 <- "S1"
  
 CHARMM>    SET chi3atom1 CB
 Parameter: CHI3ATOM1 <- "CB"
  
 CHARMM>    SET chi3atom2 SG
 Parameter: CHI3ATOM2 <- "SG"
  
 CHARMM>    SET chi3atom3 S1
 Parameter: CHI3ATOM3 <- "S1"
  
 CHARMM>    SET chi3atom4 C10
 Parameter: CHI3ATOM4 <- "C10"
  
 CHARMM>    SET chi4atom1 SG
 Parameter: CHI4ATOM1 <- "SG"
  
 CHARMM>    SET chi4atom2 S1
 Parameter: CHI4ATOM2 <- "S1"
  
 CHARMM>    SET chi4atom3 C10
 Parameter: CHI4ATOM3 <- "C10"
  
 CHARMM>    SET chi4atom4 C3
 Parameter: CHI4ATOM4 <- "C3"
  
 CHARMM>    SET chi5atom1 S1
 Parameter: CHI5ATOM1 <- "S1"
  
 CHARMM>    SET chi5atom2 C10
 Parameter: CHI5ATOM2 <- "C10"
  
 CHARMM>    SET chi5atom3 C3
 Parameter: CHI5ATOM3 <- "C3"
  
 CHARMM>    SET chi5atom4 C2
 Parameter: CHI5ATOM4 <- "C2"
  
 CHARMM>    SET chi6atom1 Dummy
 Parameter: CHI6ATOM1 <- "DUMMY"
  
 CHARMM>    SET chi6atom2 Dummy
 Parameter: CHI6ATOM2 <- "DUMMY"
  
 CHARMM>    SET chi6atom3 Dummy
 Parameter: CHI6ATOM3 <- "DUMMY"
  
 CHARMM>    SET chi6atom4 Dummy
 Parameter: CHI6ATOM4 <- "DUMMY"
  
 CHARMM>    SET chi7atom1 Dummy
 Parameter: CHI7ATOM1 <- "DUMMY"
  
 CHARMM>    SET chi7atom2 Dummy
 Parameter: CHI7ATOM2 <- "DUMMY"
  
 CHARMM>    SET chi7atom3 Dummy
 Parameter: CHI7ATOM3 <- "DUMMY"
  
 CHARMM>    SET chi7atom4 Dummy
 Parameter: CHI7ATOM4 <- "DUMMY"
  
 CHARMM>    ! set variable names for nitroxide moeity atoms
 CHARMM>    SET nitroxc1 C2
 Parameter: NITROXC1 <- "C2"
  
 CHARMM>    SET nitroxc2 C5
 Parameter: NITROXC2 <- "C5"
  
 CHARMM>    SET nitroxn N1
 Parameter: NITROXN <- "N1"
  
 CHARMM>    SET nitroxo O1
 Parameter: NITROXO <- "O1"
  
 VCLOSE: Closing unit   18 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! Set the rmsd tolerance for whether or not two
 CHARMM>    ! structures are identical. If the rmsd is less
 CHARMM>    ! than this value the two structures are considered
 CHARMM>    ! duplicates.
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>    ! Set the maximum number of continuous duplications
 CHARMM>    ! allowed before re-randomizing all torsion angles.
 CHARMM>    ! If the program generates maxdups number of minimum
 CHARMM>    ! energy structures that have already been visited
 CHARMM>    ! then a larger perturbation is applied.
 CHARMM>    SET maxdups 20
 Parameter: MAXDUPS <- "20"
  
 CHARMM>    ! Set the maximum number of rejected structures
 CHARMM>    ! allowed before re-randomizing all torsion angles.
 CHARMM>    ! If the program generates maxrejects  number of minimum
 CHARMM>    ! energy structures that are rejected
 CHARMM>    ! then a larger perturbation is applied.
 CHARMM>    SET maxrejects 20
 Parameter: MAXREJECTS <- "20"
  
 CHARMM>    ! Set the number of times the torsion angles are re-randomized
 CHARMM>    SET maxsims 1000
 Parameter: MAXSIMS <- "1000"
  
 CHARMM>    ! Set the parameters for termination of minimizations
 CHARMM>    ! vtol sets TOLENR = tolerance applied to total energy change.
 CHARMM>    ! If the energy change is less than or equal to TOLENR, the
 CHARMM>    ! minimization routine will exit.
 CHARMM>    SET vtol 0.0		! CHARMM default is 0.0
 Parameter: VTOL <- "0.0"
  
 CHARMM>    ! gtol sets TOLGRD = tolerance applied to the average gradient.
 CHARMM>    ! If the average gradient is less than or equal to TOLGRD, the
 CHARMM>    ! minimization routine will exit.
 CHARMM>    SET gtol 0.1		! CHARMM default is 0.0
 Parameter: GTOL <- "0.1"
  
 CHARMM>    ! sdsteps sets the maximum number (NSTEP) of Steepest Descents steps allowed
 CHARMM>    ! if the number of iterations exceeds NSTEP, the minimizaitn routine exits.
 CHARMM>    SET sdsteps 200
 Parameter: SDSTEPS <- "200"
  
 CHARMM>    ! abnrsteps sets the maximum number (NSTEP) of ABNR minimization cycles
 CHARMM>    ! if the number of iterations exceeds NSTEP, the minimizaitn routine exits.
 CHARMM>    SET abnrsteps 2000
 Parameter: ABNRSTEPS <- "2000"
  
 CHARMM>    ! Set up non-bonded interaction parameters
 CHARMM>    ! CUTNB: distance cutoff in generating list of pairs
 CHARMM>    ! CTOFNB: cut at which the switching function eliminates all pair contributions
 CHARMM>    ! CTONNB: cut at which smoothing function begins to reduce a pair's contribution
 CHARMM>    ! RDIE uses a distance dependent dielectric = EPSilon*distance between atom pairs
 CHARMM>    ! CDIE uses a constant dielectric
 CHARMM>    NBOND CUTNb 11.0 CTONnb 9.0 CTOFnb 10.0 -
 CHARMM>    RDIE EPSilon 2.0 SWITch VSWItch

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
   137681 ATOM PAIRS WERE FOUND FOR ATOM LIST
    12895 GROUP PAIRS REQUIRED ATOM SEARCHES

  
 CHARMM>     
  
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM     5
  
 CHARMM>    CLOSE UNIT 20
 CLOLGU>  *****  WARNING  ***** Attempt to close unit that was not open.
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for WRITE access to mmcm.ene
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> *  THIS FILE CONTAINS THE ENERGIES FROM MMC-MINIMIZATION RUN
 RDTITL> *  VTOT, VBOND, VANGL, VDIHE, VVDW, VELEC, VHBON
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RANDOM UNIFORM ISEED @seed
 Parameter: SEED -> "928338"
DIST= UNIF     SEED=     928338     SIGMA=    1.000    
    SCALE=    1.000         OFFSET=   0.0000E+00
  
 CHARMM>    SET sims 1
 Parameter: SIMS <- "1"
  
 CHARMM>    SET rejects 0
 Parameter: REJECTS <- "0"
  
 CHARMM>    SET accepts 0
 Parameter: ACCEPTS <- "0"
  
 CHARMM>    SET kb 0.001987
 Parameter: KB <- "0.001987"
  
 CHARMM>    CALC beta = 1/(@kb * @T)
 Parameter: KB -> "0.001987"
 Parameter: T -> "500"
Evaluating: 1/(0.001987*500)
 Parameter: BETA <- "1.00654"
  
 CHARMM>     
  
 CHARMM>    LABEL mainloop
  
 CHARMM>    OPEN READ UNIT 19 CARD NAME $SL_MOD/charmm/charmm_mmcm_str/mmcm.str
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mmcm.str::
 OPNLGU> Unit 19 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mmcm.str
  
 CHARMM>    STREAM UNIT 19

                    INPUT STREAM SWITCHING TO UNIT    19
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chng change
 Parameter: CHNG <- "CHANGE"
  
 CHARMM>    SET seed1 ?RAND
 RDCMND substituted energy or value "?RAND" to "0.265516"
 Parameter: SEED1 <- "0.265516"
  
 CHARMM>    CALC seed2 = int(@seed1 * 1000000)
 Parameter: SEED1 -> "0.265516"
Evaluating: INT(0.265516*1000000)
 Parameter: SEED2 <- "265516"
  
 CHARMM>    RANDom UNIForm ISEED @seed2
 Parameter: SEED2 -> "265516"
DIST= UNIF     SEED=     265516     SIGMA=    1.000    
    SCALE=    1.000         OFFSET=   0.0000E+00
  
 CHARMM>    SET iterations 0         ! set counter for number of iterations
 Parameter: ITERATIONS <- "0"
  
 CHARMM>    SET dups 0               ! set counter for counting continuous string of duplicates
 Parameter: DUPS <- "0"
  
 CHARMM>    SET rejects 0            ! set number of rejects counter
 Parameter: REJECTS <- "0"
  
 CHARMM>    SET chichoice 0          ! set chi angle choice flag
 Parameter: CHICHOICE <- "0"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    ! generate a starting structure by performing a random rotation around
 CHARMM>    ! each bond tethering the SL to the cys
 CHARMM>     
  
 CHARMM>    SET ntors 1                  ! set chi looping variable
 Parameter: NTORS <- "1"
  
 CHARMM>    LABEL startloop
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "1"
 Parameter: CHICHOICE <- "1"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "1"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "1"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "1"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "1"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "1"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 7.802626E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.387357"
 Parameter: CHI <- "0.387357"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "0.387357"
Evaluating: (0.387357*360)-180.0
 Parameter: CHI1 <- "-40.5515"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "-40.5515"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "2"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "2"
 Parameter: CHICHOICE <- "2"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "2"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "2"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "2"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "2"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "2"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.302728
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.948428"
 Parameter: CHI <- "0.948428"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.948428"
Evaluating: (0.948428*360)-180.0
 Parameter: CHI2 <- "161.434"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "161.434"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "3"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "3"
 Parameter: CHICHOICE <- "3"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "3"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "3"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "3"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "3"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "3"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.225809
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.167317"
 Parameter: CHI <- "0.167317"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.167317"
Evaluating: (0.167317*360)-180.0
 Parameter: CHI3 <- "-119.766"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "-119.766"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "4"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "4"
 Parameter: CHICHOICE <- "4"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "4"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "4"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "4"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "4"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "4"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 9.83188E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.444164"
 Parameter: CHI <- "0.444164"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.444164"
Evaluating: (0.444164*360)-180.0
 Parameter: CHI4 <- "-20.101"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "-20.101"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "5"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "5"
 Parameter: BONDS -> "5"
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "5"
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "5"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "5"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "5"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "5"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "5"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 6.449211E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.918959"
 Parameter: CHI <- "0.918959"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.918959"
Evaluating: (0.918959*360)-180.0
 Parameter: CHI5 <- "150.825"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "150.825"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "6"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "6"
 Parameter: BONDS -> "5"
 Comparing "6" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET ntors 1                  ! reset chi looping variable
 Parameter: NTORS <- "1"
  
 CHARMM>     
  
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2421 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0*************      0.00000*************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      7.41124      0.04830
MINI EXTERN>  *************    -80.75800      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2410 ATOM PAIRS WERE FOUND FOR ATOM LIST
      281 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2414 ATOM PAIRS WERE FOUND FOR ATOM LIST
      290 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2383 ATOM PAIRS WERE FOUND FOR ATOM LIST
      301 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2368 ATOM PAIRS WERE FOUND FOR ATOM LIST
      304 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2365 ATOM PAIRS WERE FOUND FOR ATOM LIST
      309 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  12964.42472*************    814.50222      0.05547
MINI INTERN>     4946.64081    317.77595      0.00000      5.96954      6.24719
MINI EXTERN>     7689.01937     -1.22814      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        25
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.40 A. APART

 General atom nonbond list generation found:
     2338 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  10971.63178   1992.79293    224.34860      0.01113
MINI INTERN>     4618.66354    277.44907      0.00000      4.58282      8.05563
MINI EXTERN>     6063.55940     -0.67868      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2308 ATOM PAIRS WERE FOUND FOR ATOM LIST
      314 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  10304.73389    666.89789    150.94218      0.00536
MINI INTERN>     4541.90455    276.18450      0.00000      4.14056     10.37444
MINI EXTERN>     5472.34492     -0.21508      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        69
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.48 A. APART

 General atom nonbond list generation found:
     2291 ATOM PAIRS WERE FOUND FOR ATOM LIST
      320 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  10023.42879    281.30510    241.87162      0.00619
MINI INTERN>     4404.38896    265.05449      0.00000      4.05935     12.01706
MINI EXTERN>     5337.72656      0.18236      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100   9760.36970    263.05909    262.42846      0.00715
MINI INTERN>     4239.44635    252.72436      0.00000      4.08278     14.03134
MINI EXTERN>     5249.49686      0.58802      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       109
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.48 A. APART

 General atom nonbond list generation found:
     2244 ATOM PAIRS WERE FOUND FOR ATOM LIST
      322 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120   9475.36582    285.00389    322.01074      0.00827
MINI INTERN>     4046.05808    238.86158      0.00000      4.13806     17.16144
MINI EXTERN>     5168.25132      0.89534      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140   9125.53006    349.83576    389.03639      0.00955
MINI INTERN>     3801.40032    221.67202      0.00000      4.21567     22.24252
MINI EXTERN>     5074.84826      1.15126      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       150
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.44 A. APART

 General atom nonbond list generation found:
     2207 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160   8674.72016    450.80990    128.98439      0.00460
MINI INTERN>     3546.70271    207.00248      0.00000      4.34745     27.70126
MINI EXTERN>     4887.39131      1.57496      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   8279.39100    395.32916    117.35101      0.00531
MINI INTERN>     3321.29402    199.43793      0.00000      4.50823     30.21780
MINI EXTERN>     4721.84858      2.08444      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       186
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.47 A. APART

 General atom nonbond list generation found:
     2167 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200   7932.57875    346.81225    140.22679      0.00614
MINI INTERN>     3127.11007    199.87491      0.00000      4.65481     28.96654
MINI EXTERN>     4569.53885      2.43358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   7932.57875    346.81225    140.22679      0.00737
STPD INTERN>     3127.11007    199.87491      0.00000      4.65481     28.96654
STPD EXTERN>     4569.53885      2.43358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2167 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.48 A. APART

 General atom nonbond list generation found:
     2148 ATOM PAIRS WERE FOUND FOR ATOM LIST
      312 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   7932.57875    346.81225    140.22679      0.00000
MINI INTERN>     3127.11007    199.87491      0.00000      4.65481     28.96654
MINI EXTERN>     4569.53885      2.43358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.50 A. APART

 General atom nonbond list generation found:
     2090 ATOM PAIRS WERE FOUND FOR ATOM LIST
      302 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.47 A. APART

 General atom nonbond list generation found:
     2046 ATOM PAIRS WERE FOUND FOR ATOM LIST
      300 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.46 A. APART

 General atom nonbond list generation found:
     2025 ATOM PAIRS WERE FOUND FOR ATOM LIST
      296 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2034 ATOM PAIRS WERE FOUND FOR ATOM LIST
      298 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.45 A. APART

 General atom nonbond list generation found:
     2035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      286 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.47 A. APART

 General atom nonbond list generation found:
     2041 ATOM PAIRS WERE FOUND FOR ATOM LIST
      288 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   5676.74988   2255.82886    410.89973      0.08579
MINI INTERN>     1545.09369    339.53930      0.00000      3.38962      0.49179
MINI EXTERN>     3788.97166     -0.73617      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.46 A. APART

 General atom nonbond list generation found:
     2052 ATOM PAIRS WERE FOUND FOR ATOM LIST
      280 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.49 A. APART

 General atom nonbond list generation found:
     2057 ATOM PAIRS WERE FOUND FOR ATOM LIST
      281 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS
 WARNING: ATOMS 1    62   THR  H    AND 1    64   CMTS C8   ONLY 1.43 A. APART

 General atom nonbond list generation found:
     2074 ATOM PAIRS WERE FOUND FOR ATOM LIST
      284 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   5129.62665    547.12323    286.88456      0.04254
MINI INTERN>     1371.81413    167.68777      0.00000      7.42279      7.80973
MINI EXTERN>     3575.13975     -0.24751      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2089 ATOM PAIRS WERE FOUND FOR ATOM LIST
      282 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2151 ATOM PAIRS WERE FOUND FOR ATOM LIST
      280 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   4873.48735    256.13931     81.29475      0.01635
MINI INTERN>     1258.46868     42.87356      0.00000      4.66815      5.47607
MINI EXTERN>     3562.22499     -0.22410      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2161 ATOM PAIRS WERE FOUND FOR ATOM LIST
      280 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   4852.29670     21.19064     42.53455      0.00808
MINI INTERN>     1240.48203     42.04213      0.00000      4.51223      4.26398
MINI EXTERN>     3561.45724     -0.46089      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        86
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2167 ATOM PAIRS WERE FOUND FOR ATOM LIST
      280 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        99
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2172 ATOM PAIRS WERE FOUND FOR ATOM LIST
      278 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   4842.54577      9.75094     42.45315      0.00913
MINI INTERN>     1239.90044     41.21978      0.00000      4.11836      3.11015
MINI EXTERN>     3554.64413     -0.44709      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120   4839.86662      2.67915     11.74985      0.00206
MINI INTERN>     1236.40126     39.83816      0.00000      3.70897      3.37106
MINI EXTERN>     3556.94246     -0.39529      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140   4838.59520      1.27142     44.54320      0.00849
MINI INTERN>     1235.88850     39.20610      0.00000      3.40982      3.19702
MINI EXTERN>     3557.02774     -0.13399      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       157
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2173 ATOM PAIRS WERE FOUND FOR ATOM LIST
      282 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160   4837.29844      1.29676     36.32618      0.00468
MINI INTERN>     1235.14546     36.33953      0.00000      3.28900      3.15796
MINI EXTERN>     3559.40297     -0.03647      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   4835.18611      2.11233      5.68268      0.00247
MINI INTERN>     1237.39328     38.74685      0.00000      3.12675      2.69201
MINI EXTERN>     3553.06901      0.15820      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       194
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2166 ATOM PAIRS WERE FOUND FOR ATOM LIST
      285 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200   4834.14901      1.03710      3.89039      0.00139
MINI INTERN>     1238.15874     38.58834      0.00000      3.26655      1.98878
MINI EXTERN>     3552.11907      0.02754      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220   4833.96088      0.18813      2.82234      0.00047
MINI INTERN>     1237.07519     38.76643      0.00000      3.16023      1.83708
MINI EXTERN>     3553.16605     -0.04410      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240   4833.92198      0.03890      0.62694      0.00026
MINI INTERN>     1237.30418     38.92821      0.00000      3.08330      1.76028
MINI EXTERN>     3552.91010     -0.06408      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260   4833.90096      0.02103      0.44314      0.00025
MINI INTERN>     1237.36002     38.78791      0.00000      3.06240      1.80548
MINI EXTERN>     3552.93484     -0.04970      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280   4833.89924      0.00171      0.20887      0.00005
MINI INTERN>     1237.40135     38.76323      0.00000      3.06273      1.80551
MINI EXTERN>     3552.91551     -0.04909      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      282   4833.89918      0.00006      0.03462      0.00004
ABNR INTERN>     1237.41385     38.77416      0.00000      3.06181      1.80278
ABNR EXTERN>     3552.89597     -0.04939      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    STREAM UNIT 35

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "1"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "1"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frame1out.str::
 OPNLGU> Unit 81 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frame1out.str
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "1"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    81
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "1"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame1.crd
  
 CHARMM>    WRITE COOR UNIT 51 CARD
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   81 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "1"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * 4833.9 1237.41 38.7742 3.06181 3552.9 -4.938792E-02
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "4833.9"
 Parameter: ELAST <- "4833.9"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>     
  
 CHARMM>    LABEL mcloop
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.937607"
 Parameter: CHICHOICE1 <- "0.937607"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.937607"
 Parameter: BONDS -> "5"
Evaluating: INT(0.937607*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.357446
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.594838"
 Parameter: CHI <- "0.594838"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.594838"
Evaluating: (0.594838*360)-180.0
 Parameter: CHI4 <- "34.1417"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "34.1417"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2774 ATOM PAIRS WERE FOUND FOR ATOM LIST
      276 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      6.93873      0.04830
MINI EXTERN>  *************     29.29126      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2735 ATOM PAIRS WERE FOUND FOR ATOM LIST
      279 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2704 ATOM PAIRS WERE FOUND FOR ATOM LIST
      285 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2656 ATOM PAIRS WERE FOUND FOR ATOM LIST
      282 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2654 ATOM PAIRS WERE FOUND FOR ATOM LIST
      283 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2645 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2646 ATOM PAIRS WERE FOUND FOR ATOM LIST
      288 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  21833.93985*************   2632.95219      0.05547
MINI INTERN>     6758.93565    529.67047      0.00000      6.83858     16.67446
MINI EXTERN>    14520.37305      1.44764      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        39
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2599 ATOM PAIRS WERE FOUND FOR ATOM LIST
      278 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  17665.77892   4168.16094    530.33589      0.01113
MINI INTERN>     5689.56037    540.37139      0.00000      7.23816     26.51452
MINI EXTERN>    11401.74321      0.35126      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60  16804.25874    861.52017    847.02221      0.01286
MINI INTERN>     5165.49577    603.81619      0.00000      7.76486     19.32691
MINI EXTERN>    11006.41352      1.44149      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2569 ATOM PAIRS WERE FOUND FOR ATOM LIST
      284 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  16065.19393    739.06482    370.54718      0.00619
MINI INTERN>     4908.09229    645.05251      0.00000      8.19394     14.11206
MINI EXTERN>    10487.69926      2.04385      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  15584.90705    480.28688    486.90683      0.00715
MINI INTERN>     4804.11274    668.07289      0.00000      8.50698     11.48161
MINI EXTERN>    10090.51016      2.22268      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       103
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2554 ATOM PAIRS WERE FOUND FOR ATOM LIST
      287 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  15302.15807    282.74898    106.75614      0.00344
MINI INTERN>     4723.39431    674.68411      0.00000      8.71104      9.90662
MINI EXTERN>     9883.30547      2.15652      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  15126.61185    175.54622    244.10416      0.00398
MINI INTERN>     4608.51617    676.85527      0.00000      8.83067      8.78423
MINI EXTERN>     9821.44502      2.18050      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       159
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2552 ATOM PAIRS WERE FOUND FOR ATOM LIST
      290 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  14983.19658    143.41527    275.09864      0.00460
MINI INTERN>     4508.28462    679.30095      0.00000      8.84828      8.13188
MINI EXTERN>     9776.41773      2.21311      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  14868.75770    114.43888    325.00104      0.00531
MINI INTERN>     4424.03412    681.33598      0.00000      8.80377      7.74178
MINI EXTERN>     9744.61343      2.22862      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  14745.18402    123.57368     78.27482      0.00256
MINI INTERN>     4346.81189    683.06606      0.00000      8.72225      7.49257
MINI EXTERN>     9696.86288      2.22836      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  14745.18402    123.57368     78.27482      0.00307
STPD INTERN>     4346.81189    683.06606      0.00000      8.72225      7.49257
STPD EXTERN>     9696.86288      2.22836      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2552 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2558 ATOM PAIRS WERE FOUND FOR ATOM LIST
      290 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  14745.18402    123.57368     78.27482      0.00000
MINI INTERN>     4346.81189    683.06606      0.00000      8.72225      7.49257
MINI EXTERN>     9696.86288      2.22836      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2563 ATOM PAIRS WERE FOUND FOR ATOM LIST
      292 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2566 ATOM PAIRS WERE FOUND FOR ATOM LIST
      297 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  14185.71007    559.47395     89.60143      0.02169
MINI INTERN>     3941.47499    636.03858      0.00000      7.37767      7.55104
MINI EXTERN>     9591.20501      2.06278      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2572 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  14091.68432     94.02575     29.99044      0.01221
MINI INTERN>     3861.37786    587.71741      0.00000      6.95532      6.97175
MINI EXTERN>     9627.21944      1.44253      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2569 ATOM PAIRS WERE FOUND FOR ATOM LIST
      300 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  14048.16121     43.52311     37.96186      0.00687
MINI INTERN>     3837.28301    584.27524      0.00000      6.48229      7.13233
MINI EXTERN>     9611.83164      1.15670      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2571 ATOM PAIRS WERE FOUND FOR ATOM LIST
      306 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        70
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2564 ATOM PAIRS WERE FOUND FOR ATOM LIST
      309 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  14016.92216     31.23905     11.79080      0.00387
MINI INTERN>     3818.38911    582.44035      0.00000      7.15379      7.63012
MINI EXTERN>     9600.02124      1.28755      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  14014.64397      2.27819      6.21909      0.00131
MINI INTERN>     3801.63364    592.53222      0.00000      7.41124      6.80638
MINI EXTERN>     9604.86593      1.39456      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       111
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2560 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       119
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2576 ATOM PAIRS WERE FOUND FOR ATOM LIST
      304 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       120
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2565 ATOM PAIRS WERE FOUND FOR ATOM LIST
      309 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  13999.74426     14.89971     48.99721      0.00934
MINI INTERN>     3690.11906    643.10281      0.00000      9.40842      7.21319
MINI EXTERN>     9647.96795      1.93282      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       128
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2580 ATOM PAIRS WERE FOUND FOR ATOM LIST
      304 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  13912.03138     87.71288    183.84490      0.01923
MINI INTERN>     3572.21339    649.40994      0.00000     10.20420      7.40127
MINI EXTERN>     9670.90687      1.89571      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       141
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2588 ATOM PAIRS WERE FOUND FOR ATOM LIST
      305 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  13867.01954     45.01184     61.31123      0.00950
MINI INTERN>     3558.66634    639.96252      0.00000      8.29570      7.03581
MINI EXTERN>     9651.30041      1.75877      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       172
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2587 ATOM PAIRS WERE FOUND FOR ATOM LIST
      305 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180  13850.79460     16.22495     52.42110      0.00594
MINI INTERN>     3537.32011    641.76487      0.00000      8.42804      7.03145
MINI EXTERN>     9654.43775      1.81237      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  13844.39494      6.39965     13.50208      0.00201
MINI INTERN>     3518.38814    655.08651      0.00000      8.23442      6.70514
MINI EXTERN>     9654.23489      1.74584      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  13843.00471      1.39023      6.15473      0.00113
MINI INTERN>     3503.00922    663.27657      0.00000      8.27750      6.80748
MINI EXTERN>     9659.99268      1.64125      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240  13842.52161      0.48310      6.86036      0.00106
MINI INTERN>     3507.81120    658.66189      0.00000      8.51666      6.75412
MINI EXTERN>     9659.10805      1.66969      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260  13842.00022      0.52138     29.93416      0.00276
MINI INTERN>     3511.67560    655.06057      0.00000      8.92392      6.89611
MINI EXTERN>     9657.78251      1.66152      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       269
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2596 ATOM PAIRS WERE FOUND FOR ATOM LIST
      302 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      280  13841.58318      0.41704      4.08628      0.00104
MINI INTERN>     3513.27175    654.12475      0.00000      9.20430      6.99137
MINI EXTERN>     9656.33389      1.65712      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300  13841.46537      0.11781      1.34995      0.00035
MINI INTERN>     3509.78653    656.22688      0.00000      9.39047      6.96194
MINI EXTERN>     9657.44538      1.65417      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      320  13841.42460      0.04076      1.94447      0.00020
MINI INTERN>     3508.24394    656.77738      0.00000      9.43999      6.94554
MINI EXTERN>     9658.36044      1.65731      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      340  13841.41515      0.00945      0.55043      0.00018
MINI INTERN>     3508.23396    657.13709      0.00000      9.51105      6.92220
MINI EXTERN>     9657.95262      1.65823      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      360  13841.40915      0.00600      0.78452      0.00017
MINI INTERN>     3508.27819    656.75598      0.00000      9.57348      6.90131
MINI EXTERN>     9658.24210      1.65808      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      380  13841.40421      0.00494      0.14624      0.00004
MINI INTERN>     3508.51918    656.60968      0.00000      9.65887      6.90790
MINI EXTERN>     9658.04967      1.65891      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      400  13841.40365      0.00056      0.23441      0.00003
MINI INTERN>     3508.61261    656.54115      0.00000      9.67478      6.91171
MINI EXTERN>     9658.00435      1.65905      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      401  13841.40356      0.00009      0.08188      0.00004
ABNR INTERN>     3508.66182    656.50714      0.00000      9.67910      6.90746
ABNR EXTERN>     9657.98900      1.65904      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "4833.9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "13841.4"
 Comparing "13841.4" and "4833.9".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "4833.9"
 RDCMND substituted energy or value "?ENER" to "13841.4"
 Comparing "13841.4" and "4833.9".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "4833.9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "13841.4"
 Comparing "13841.4" and "4833.9".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "4833.9"
 RDCMND substituted energy or value "?ENER" to "13841.4"
 Comparing "13841.4" and "4833.9".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.448499"
 Parameter: R <- "0.448499"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "4833.9"
 RDCMND substituted energy or value "?ENER" to "13841.4"
Evaluating: 13841.4-4833.9
 Parameter: DELE <- "9007.5"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "9007.5"
Evaluating: 1.00654*9007.5
 Parameter: BETADELE <- "9066.41"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "9066.41"
Evaluating: EXP(-9066.41)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.448499"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.448499".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.448499"
 Comparing "0" and "0.448499".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "1"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "1"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "1"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "1" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.91949"
 Parameter: CHICHOICE1 <- "0.91949"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.91949"
 Parameter: BONDS -> "5"
Evaluating: INT(0.91949*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.876534
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.899863"
 Parameter: CHI <- "0.899863"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.899863"
Evaluating: (0.899863*360)-180.0
 Parameter: CHI4 <- "143.951"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "143.951"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2397 ATOM PAIRS WERE FOUND FOR ATOM LIST
      262 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        01401120.11257*************2196613.66011      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      6.86358      0.04830
MINI EXTERN>  1401091.21934     -0.01569      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2397 ATOM PAIRS WERE FOUND FOR ATOM LIST
      258 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2395 ATOM PAIRS WERE FOUND FOR ATOM LIST
      249 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2371 ATOM PAIRS WERE FOUND FOR ATOM LIST
      240 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2372 ATOM PAIRS WERE FOUND FOR ATOM LIST
      238 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2346 ATOM PAIRS WERE FOUND FOR ATOM LIST
      234 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2331 ATOM PAIRS WERE FOUND FOR ATOM LIST
      236 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2298 ATOM PAIRS WERE FOUND FOR ATOM LIST
      232 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2263 ATOM PAIRS WERE FOUND FOR ATOM LIST
      241 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2256 ATOM PAIRS WERE FOUND FOR ATOM LIST
      234 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    231.971561400888.14101     41.14733      0.05547
MINI INTERN>       34.66155     99.75336      0.00000      6.93299      3.46996
MINI EXTERN>       87.55791     -0.40420      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        25
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2198 ATOM PAIRS WERE FOUND FOR ATOM LIST
      234 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2154 ATOM PAIRS WERE FOUND FOR ATOM LIST
      240 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     66.13948    165.83208     11.84202      0.01113
MINI INTERN>        4.88181     32.26850      0.00000      7.02672      0.19447
MINI EXTERN>       22.23987     -0.47189      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     38.29649     27.84299      5.39085      0.00536
MINI INTERN>        2.54013     19.78773      0.00000      7.85610      0.13880
MINI EXTERN>        8.63788     -0.66415      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2104 ATOM PAIRS WERE FOUND FOR ATOM LIST
      236 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     27.89379     10.40270      8.78591      0.00619
MINI INTERN>        2.20635     15.51479      0.00000      8.36149      0.43757
MINI EXTERN>        2.10052     -0.72692      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     22.10318      5.79062      2.33066      0.00298
MINI INTERN>        1.87067     13.17644      0.00000      8.65960      0.60261
MINI EXTERN>       -1.52014     -0.68601      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     19.01698      3.08620      4.96532      0.00344
MINI INTERN>        1.97410     12.01025      0.00000      8.83169      0.63371
MINI EXTERN>       -3.82276     -0.61001      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     16.77587      2.24110      1.70823      0.00166
MINI INTERN>        1.48798     11.53947      0.00000      8.87890      0.57990
MINI EXTERN>       -5.16724     -0.54314      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     15.08816      1.68771      1.51561      0.00192
MINI INTERN>        1.38869     10.97592      0.00000      8.78165      0.50912
MINI EXTERN>       -6.08659     -0.48062      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       164
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2033 ATOM PAIRS WERE FOUND FOR ATOM LIST
      237 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     13.56967      1.51850      7.53676      0.00531
MINI INTERN>        1.94561      9.89063      0.00000      8.43800      0.42738
MINI EXTERN>       -6.69749     -0.43445      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     10.91096      2.65870      3.20048      0.00256
MINI INTERN>        1.28345      8.77427      0.00000      7.91148      0.33901
MINI EXTERN>       -6.94167     -0.45559      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     10.91096      2.65870      3.20048      0.00307
STPD INTERN>        1.28345      8.77427      0.00000      7.91148      0.33901
STPD EXTERN>       -6.94167     -0.45559      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2033 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2018 ATOM PAIRS WERE FOUND FOR ATOM LIST
      233 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     10.91096      2.65870      3.20048      0.00000
MINI INTERN>        1.28345      8.77427      0.00000      7.91148      0.33901
MINI EXTERN>       -6.94167     -0.45559      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1976 ATOM PAIRS WERE FOUND FOR ATOM LIST
      229 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1928 ATOM PAIRS WERE FOUND FOR ATOM LIST
      227 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20      1.59538      9.31559      5.08409      0.02288
MINI INTERN>        2.11028      7.13229      0.00000      5.49622      0.32101
MINI EXTERN>      -12.82677     -0.63765      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        34
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1889 ATOM PAIRS WERE FOUND FOR ATOM LIST
      226 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -2.65425      4.24963      2.37004      0.01288
MINI INTERN>        0.74509      5.11368      0.00000      4.73353      0.21828
MINI EXTERN>      -12.93751     -0.52732      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1859 ATOM PAIRS WERE FOUND FOR ATOM LIST
      226 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1812 ATOM PAIRS WERE FOUND FOR ATOM LIST
      221 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -5.90953      3.25528      2.47199      0.01208
MINI INTERN>        0.20766      2.64917      0.00000      4.75044      0.09891
MINI EXTERN>      -13.14939     -0.46632      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        66
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1767 ATOM PAIRS WERE FOUND FOR ATOM LIST
      219 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -7.01220      1.10267      0.56150      0.00408
MINI INTERN>        0.14126      1.86338      0.00000      4.95286      0.04911
MINI EXTERN>      -13.36608     -0.65271      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -7.23768      0.22548      0.75103      0.00383
MINI INTERN>        0.10755      1.85848      0.00000      4.90889      0.04161
MINI EXTERN>      -13.50501     -0.64920      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       108
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1746 ATOM PAIRS WERE FOUND FOR ATOM LIST
      217 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       118
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1739 ATOM PAIRS WERE FOUND FOR ATOM LIST
      221 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -8.01442      0.77674      1.55641      0.00598
MINI INTERN>        0.29641      1.72604      0.00000      4.87501      0.00851
MINI EXTERN>      -14.27476     -0.64563      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -8.14442      0.13000      0.35756      0.00180
MINI INTERN>        0.10512      1.64931      0.00000      4.83772      0.00412
MINI EXTERN>      -14.08407     -0.65663      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -8.17676      0.03234      0.17179      0.00101
MINI INTERN>        0.10023      1.62044      0.00000      4.89144      0.00540
MINI EXTERN>      -14.12841     -0.66586      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      166     -8.17949      0.00272      0.09126      0.00081
ABNR INTERN>        0.10446      1.61005      0.00000      4.88989      0.00622
ABNR EXTERN>      -14.12542     -0.66469      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "4833.9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.17949"
 Comparing "-8.17949" and "4833.9".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "4833.9"
 RDCMND substituted energy or value "?ENER" to "-8.17949"
 Comparing "-8.17949" and "4833.9".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    174.1142  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.526574
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.52657"
 Parameter: RMSD <- "3.52657"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.52657"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52657" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.52657"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52657" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.52657"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52657" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "1"
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "4833.9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.17949"
 Comparing "-8.17949" and "4833.9".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "4833.9"
 RDCMND substituted energy or value "?ENER" to "-8.17949"
 Comparing "-8.17949" and "4833.9".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "3.52657"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3.52657" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "3.52657"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52657" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "2"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "2"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "2"
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "2"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "2" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "2"
 Comparing "2" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "2"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame2.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -8.17949 0.104455 1.61005 4.88989 -14.1254 -0.664686
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-8.17949"
 Parameter: ELAST <- "-8.17949"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "2"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "1"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "1" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.99161"
 Parameter: CHICHOICE1 <- "0.99161"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.99161"
 Parameter: BONDS -> "5"
Evaluating: INT(0.99161*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.989926
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.683537"
 Parameter: CHI <- "0.683537"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.683537"
Evaluating: (0.683537*360)-180.0
 Parameter: CHI4 <- "66.0733"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "66.0733"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2815 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      5.68947      0.04830
MINI EXTERN>  *************      4.48516      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2828 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2830 ATOM PAIRS WERE FOUND FOR ATOM LIST
      317 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2841 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2847 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2835 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2824 ATOM PAIRS WERE FOUND FOR ATOM LIST
      329 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2798 ATOM PAIRS WERE FOUND FOR ATOM LIST
      337 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2785 ATOM PAIRS WERE FOUND FOR ATOM LIST
      333 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2796 ATOM PAIRS WERE FOUND FOR ATOM LIST
      338 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2805 ATOM PAIRS WERE FOUND FOR ATOM LIST
      338 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20 378956.17809************* 764005.18600      0.13312
MINI INTERN>     4740.15289    172.24825      0.00000      7.28723      4.66225
MINI EXTERN>   374027.35079      4.47668      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2787 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2806 ATOM PAIRS WERE FOUND FOR ATOM LIST
      332 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  14313.93847 364642.23962    528.35261      0.01113
MINI INTERN>     5322.79041    229.34446      0.00000      8.35421      4.16364
MINI EXTERN>     8748.19767      1.08808      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2761 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  13915.83323    398.10524    223.51835      0.00536
MINI INTERN>     5088.61368    211.89184      0.00000      8.57667      3.88881
MINI EXTERN>     8602.05330      0.80892      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  13708.48116    207.35207    245.40361      0.00619
MINI INTERN>     4938.04731    209.42412      0.00000      8.48893      3.62924
MINI EXTERN>     8548.26873      0.62283      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  13531.08253    177.39863    105.09476      0.00298
MINI INTERN>     4865.88162    201.92567      0.00000      8.28722      3.37290
MINI EXTERN>     8451.16606      0.44906      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       104
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2759 ATOM PAIRS WERE FOUND FOR ATOM LIST
      326 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  13394.78778    136.29476    134.81162      0.00344
MINI INTERN>     4753.42748    201.39387      0.00000      8.04200      3.18299
MINI EXTERN>     8428.42262      0.31883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  13273.71750    121.07028    180.25111      0.00398
MINI INTERN>     4647.04806    202.83973      0.00000      7.79027      3.01767
MINI EXTERN>     8412.81715      0.20462      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       156
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2751 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  13158.37482    115.34268    201.46245      0.00460
MINI INTERN>     4535.95878    203.76652      0.00000      7.54827      2.86971
MINI EXTERN>     8408.12419      0.10734      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  13046.74324    111.63158    231.75633      0.00531
MINI INTERN>     4423.40134    203.37059      0.00000      7.32297      2.73459
MINI EXTERN>     8409.89513      0.01863      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  13066.36927    -19.62603    906.24049      0.01474
MINI INTERN>     4179.86383    195.75930      0.00000      7.10164      2.48100
MINI EXTERN>     8681.28271     -0.11920      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  13066.36927    -19.62603    906.24049      0.00737
STPD INTERN>     4179.86383    195.75930      0.00000      7.10164      2.48100
STPD EXTERN>     8681.28271     -0.11920      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2751 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2745 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  12909.16588    157.20339    329.71574      0.00000
MINI INTERN>     4263.77366    220.09911      0.00000      7.11340      2.58348
MINI EXTERN>     8415.72263     -0.12641      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2742 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2744 ATOM PAIRS WERE FOUND FOR ATOM LIST
      318 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2738 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2743 ATOM PAIRS WERE FOUND FOR ATOM LIST
      318 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  12145.31954    763.84634    441.53603      0.07053
MINI INTERN>     3449.37493    245.08321      0.00000      5.74515      1.56544
MINI EXTERN>     8444.30793     -0.75712      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2742 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2746 ATOM PAIRS WERE FOUND FOR ATOM LIST
      315 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  12056.95519     88.36434     32.60090      0.01061
MINI INTERN>     3473.02484    253.01571      0.00000      5.64642      1.55661
MINI EXTERN>     8324.51969     -0.80808      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2749 ATOM PAIRS WERE FOUND FOR ATOM LIST
      322 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        49
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2765 ATOM PAIRS WERE FOUND FOR ATOM LIST
      325 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2774 ATOM PAIRS WERE FOUND FOR ATOM LIST
      326 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2781 ATOM PAIRS WERE FOUND FOR ATOM LIST
      332 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2776 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  11892.17530    164.77989    258.75349      0.03746
MINI INTERN>     3056.13717    388.87526      0.00000      4.20097      0.99507
MINI EXTERN>     8444.32455     -2.35773      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        63
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2802 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  11564.37241    327.80289     58.26187      0.01248
MINI INTERN>     2906.15209    311.33159      0.00000      4.87962      1.74579
MINI EXTERN>     8342.67834     -2.41502      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        84
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2813 ATOM PAIRS WERE FOUND FOR ATOM LIST
      331 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        95
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2831 ATOM PAIRS WERE FOUND FOR ATOM LIST
      333 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  11521.28607     43.08634     13.50505      0.00422
MINI INTERN>     2892.44885    304.70339      0.00000      6.22099      1.85512
MINI EXTERN>     8318.17614     -2.11842      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  11513.73245      7.55362     10.19836      0.00237
MINI INTERN>     2883.08458    301.23847      0.00000      6.62033      2.14117
MINI EXTERN>     8322.69145     -2.04355      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       127
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2864 ATOM PAIRS WERE FOUND FOR ATOM LIST
      335 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       132
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2898 ATOM PAIRS WERE FOUND FOR ATOM LIST
      341 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       133
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2870 ATOM PAIRS WERE FOUND FOR ATOM LIST
      336 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  11494.86751     18.86493     80.65300      0.01131
MINI INTERN>     2884.31624    285.23084      0.00000      9.39831      3.15702
MINI EXTERN>     8314.67878     -1.91368      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       144
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2888 ATOM PAIRS WERE FOUND FOR ATOM LIST
      340 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  11481.19977     13.66775     26.03691      0.00424
MINI INTERN>     2891.32237    278.66107      0.00000     10.04663      3.73792
MINI EXTERN>     8299.33951     -1.90773      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  11473.19905      8.00072     10.06895      0.00398
MINI INTERN>     2884.77572    279.99564      0.00000     10.63719      3.89616
MINI EXTERN>     8295.59124     -1.69690      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       186
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2913 ATOM PAIRS WERE FOUND FOR ATOM LIST
      340 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200  11471.12526      2.07379      6.12267      0.00118
MINI INTERN>     2883.24319    276.70064      0.00000     10.97731      3.69770
MINI EXTERN>     8298.10366     -1.59726      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  11470.84028      0.28498      2.07449      0.00066
MINI INTERN>     2884.33692    276.69929      0.00000     11.02561      3.60693
MINI EXTERN>     8296.76859     -1.59706      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240  11470.58350      0.25678      3.02718      0.00062
MINI INTERN>     2884.42576    275.87841      0.00000     11.08066      3.44168
MINI EXTERN>     8297.34980     -1.59282      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260  11470.42716      0.15633      1.77526      0.00058
MINI INTERN>     2883.11021    275.22221      0.00000     11.11844      3.18688
MINI EXTERN>     8299.36278     -1.57336      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280  11470.38864      0.03852      0.93750      0.00020
MINI INTERN>     2882.45705    275.38945      0.00000     11.07812      3.18386
MINI EXTERN>     8299.85113     -1.57097      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300  11470.38287      0.00577      0.32520      0.00011
MINI INTERN>     2882.89111    275.48090      0.00000     11.06290      3.18816
MINI EXTERN>     8299.33192     -1.57212      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      318  11470.38171      0.00117      0.09797      0.00003
ABNR INTERN>     2882.94879    275.46646      0.00000     11.06638      3.19248
ABNR EXTERN>     8299.28144     -1.57385      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.205994"
 Parameter: R <- "0.205994"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
Evaluating: 11470.4--8.17949
 Parameter: DELE <- "11478.6"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "11478.6"
Evaluating: 1.00654*11478.6
 Parameter: BETADELE <- "11553.7"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "11553.7"
Evaluating: EXP(-11553.7)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.205994"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.205994".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.205994"
 Comparing "0" and "0.205994".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "2"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "3"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "2"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "2" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.143495"
 Parameter: CHICHOICE1 <- "0.143495"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.143495"
 Parameter: BONDS -> "5"
Evaluating: INT(0.143495*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.722305
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.776334"
 Parameter: CHI <- "0.776334"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.776334"
Evaluating: (0.776334*360)-180.0
 Parameter: CHI5 <- "99.4802"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "99.4802"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2758 ATOM PAIRS WERE FOUND FOR ATOM LIST
      295 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      5.68947      0.04830
MINI EXTERN>  *************      1.66288      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2740 ATOM PAIRS WERE FOUND FOR ATOM LIST
      295 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  88.3679 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 103.0127 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2728 ATOM PAIRS WERE FOUND FOR ATOM LIST
      292 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 108.7284 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 111.2000 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2721 ATOM PAIRS WERE FOUND FOR ATOM LIST
      302 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 111.4202 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 106.2957 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 105.8120 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  98.4009 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  97.6778 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  95.2497 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  94.9622 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  93.1256 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       20  31050.00049*************   4768.80276      0.02311
MINI INTERN>     4706.03033    435.93043      0.00000      6.20042     66.09218
MINI EXTERN>    25835.97923     -0.23208      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  92.7039 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2704 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  91.2735 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  90.3774 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.7417 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.3148 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.0489 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  88.9662 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  88.9786 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.1323 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.4161 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2699 ATOM PAIRS WERE FOUND FOR ATOM LIST
      314 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.5703 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.6390 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.6307 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.5147 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.1450 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.0246 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  88.5013 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  88.1296 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  87.7027 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  87.5412 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       40  19169.69519  11880.30531    847.30416      0.01113
MINI INTERN>     3821.80294    367.31780      0.00000      6.13235     58.40904
MINI EXTERN>    14916.81261     -0.77956      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  86.6315 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  85.9802 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  85.8432 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  85.3077 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  84.8809 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  84.5070 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        50
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2692 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        54
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2693 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2700 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2700 ATOM PAIRS WERE FOUND FOR ATOM LIST
      329 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        60
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2706 ATOM PAIRS WERE FOUND FOR ATOM LIST
      321 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   5940.07585  13229.61934    890.01250      0.07406
MINI INTERN>     2113.30549    319.00875      0.00000      7.99916     38.83903
MINI EXTERN>     3461.84713     -0.92372      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        69
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2686 ATOM PAIRS WERE FOUND FOR ATOM LIST
      325 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        79
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2687 ATOM PAIRS WERE FOUND FOR ATOM LIST
      317 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   4288.71994   1651.35591    212.10131      0.03566
MINI INTERN>     1472.17782    297.69130      0.00000      6.98840     15.44814
MINI EXTERN>     2497.40200     -0.98771      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        92
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2682 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   3940.45811    348.26183    105.18698      0.01717
MINI INTERN>     1160.25964    321.82463      0.00000      5.50107      8.42093
MINI EXTERN>     2445.76443     -1.31259      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       109
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2694 ATOM PAIRS WERE FOUND FOR ATOM LIST
      306 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120   3796.99187    143.46624     25.00823      0.00827
MINI INTERN>     1087.70342    332.37508      0.00000      5.05052      6.85681
MINI EXTERN>     2366.77207     -1.76604      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       136
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2718 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140   3715.05749     81.93439     53.93479      0.00955
MINI INTERN>     1046.57299    339.72085      0.00000      4.94137      5.35509
MINI EXTERN>     2320.35622     -1.88903      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160   3659.27985     55.77763     63.74063      0.01104
MINI INTERN>     1024.04054    342.89006      0.00000      5.05700      4.05454
MINI EXTERN>     2285.10709     -1.86936      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       178
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2749 ATOM PAIRS WERE FOUND FOR ATOM LIST
      291 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180   3605.21318     54.06668     25.61099      0.00531
MINI INTERN>      958.34877    341.91283      0.00000      5.26643      2.94277
MINI EXTERN>     2298.55950     -1.81713      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       193
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2762 ATOM PAIRS WERE FOUND FOR ATOM LIST
      291 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       199
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2776 ATOM PAIRS WERE FOUND FOR ATOM LIST
      296 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200   3154.68482    450.52836     54.30327      0.01474
MINI INTERN>      737.48195    397.63039      0.00000      5.44208      1.30048
MINI EXTERN>     2014.83959     -2.00967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   3154.68482    450.52836     54.30327      0.01768
STPD INTERN>      737.48195    397.63039      0.00000      5.44208      1.30048
STPD EXTERN>     2014.83959     -2.00967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2776 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2777 ATOM PAIRS WERE FOUND FOR ATOM LIST
      295 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   3154.68482    450.52836     54.30327      0.00000
MINI INTERN>      737.48195    397.63039      0.00000      5.44208      1.30048
MINI EXTERN>     2014.83959     -2.00967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2772 ATOM PAIRS WERE FOUND FOR ATOM LIST
      300 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2760 ATOM PAIRS WERE FOUND FOR ATOM LIST
      307 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2762 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2749 ATOM PAIRS WERE FOUND FOR ATOM LIST
      302 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2752 ATOM PAIRS WERE FOUND FOR ATOM LIST
      298 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2740 ATOM PAIRS WERE FOUND FOR ATOM LIST
      293 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2753 ATOM PAIRS WERE FOUND FOR ATOM LIST
      297 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2742 ATOM PAIRS WERE FOUND FOR ATOM LIST
      292 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   2392.50165    762.18317     28.14756      0.08579
MINI INTERN>      537.19761    409.80551      0.00000      8.45963      1.26696
MINI EXTERN>     1436.91717     -1.14523      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2753 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2771 ATOM PAIRS WERE FOUND FOR ATOM LIST
      298 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   2346.74860     45.75305      8.67057      0.01738
MINI INTERN>      518.07957    387.05849      0.00000     10.34976      1.99041
MINI EXTERN>     1430.47919     -1.20883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2768 ATOM PAIRS WERE FOUND FOR ATOM LIST
      306 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   2340.06100      6.68760     18.94261      0.02095
MINI INTERN>      506.85001    388.29367      0.00000     10.91002      1.74596
MINI EXTERN>     1433.63359     -1.37224      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80   2338.86962      1.19138      0.94369      0.00157
MINI INTERN>      507.05793    390.65281      0.00000     10.87420      1.84104
MINI EXTERN>     1429.81289     -1.36926      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>       96   2338.85261      0.01701      0.08412      0.00026
ABNR INTERN>      506.62446    390.81744      0.00000     10.88241      1.82579
ABNR EXTERN>     1430.08268     -1.38016      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "2338.85"
 Comparing "2338.85" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "2338.85"
 Comparing "2338.85" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "2338.85"
 Comparing "2338.85" and "-8.17949".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "2338.85"
 Comparing "2338.85" and "-8.17949".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.8481"
 Parameter: R <- "0.8481"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "2338.85"
Evaluating: 2338.85--8.17949
 Parameter: DELE <- "2347.03"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "2347.03"
Evaluating: 1.00654*2347.03
 Parameter: BETADELE <- "2362.38"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "2362.38"
Evaluating: EXP(-2362.38)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.8481"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.8481".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.8481"
 Comparing "0" and "0.8481".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "3"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "4"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "3"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "3" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "2.130957E-02"
 Parameter: CHICHOICE1 <- "2.130957E-02"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "2.130957E-02"
 Parameter: BONDS -> "5"
Evaluating: INT(2.130957E-02*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.149934
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.947194"
 Parameter: CHI <- "0.947194"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.947194"
Evaluating: (0.947194*360)-180.0
 Parameter: CHI5 <- "160.99"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "160.99"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2828 ATOM PAIRS WERE FOUND FOR ATOM LIST
      315 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      5.68947      0.04830
MINI EXTERN>  *************      6.27779      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2843 ATOM PAIRS WERE FOUND FOR ATOM LIST
      317 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2859 ATOM PAIRS WERE FOUND FOR ATOM LIST
      318 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2846 ATOM PAIRS WERE FOUND FOR ATOM LIST
      322 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2830 ATOM PAIRS WERE FOUND FOR ATOM LIST
      326 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2808 ATOM PAIRS WERE FOUND FOR ATOM LIST
      333 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2809 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2800 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  20807.43910*************   5089.65563      0.05547
MINI INTERN>     5201.30958    190.08408      0.00000      7.02900      1.16732
MINI EXTERN>    15405.41428      2.43484      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2809 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2790 ATOM PAIRS WERE FOUND FOR ATOM LIST
      326 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  14374.03224   6433.40686    436.13759      0.01113
MINI INTERN>     5162.63709    188.63153      0.00000      8.29593      5.07038
MINI EXTERN>     9008.03904      1.35827      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60  13995.94142    378.09081    438.88236      0.01286
MINI INTERN>     5018.89605    185.57715      0.00000      8.64374      4.81365
MINI EXTERN>     8777.06484      0.94599      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        77
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2772 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  13704.94798    290.99344    265.79951      0.00619
MINI INTERN>     5016.85899    181.79724      0.00000      8.59987      4.25316
MINI EXTERN>     8492.73545      0.70327      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  13521.49014    183.45784     97.64830      0.00298
MINI INTERN>     4851.29896    174.80170      0.00000      8.40052      3.93882
MINI EXTERN>     8482.47441      0.57572      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  13379.50823    141.98191    143.00695      0.00344
MINI INTERN>     4719.10302    177.11479      0.00000      8.13513      3.63887
MINI EXTERN>     8471.07179      0.44463      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       127
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2769 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  13255.21890    124.28933    169.39972      0.00398
MINI INTERN>     4596.42908    179.64180      0.00000      7.86227      3.39262
MINI EXTERN>     8467.56119      0.33195      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  13138.57792    116.64098    186.44479      0.00460
MINI INTERN>     4473.41994    183.14878      0.00000      7.59740      3.18031
MINI EXTERN>     8471.00265      0.22884      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       179
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2754 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180  13027.31415    111.26377    190.93733      0.00531
MINI INTERN>     4351.36622    186.50277      0.00000      7.35774      3.00031
MINI EXTERN>     8478.95117      0.13594      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  12912.26695    115.04720    264.23062      0.00614
MINI INTERN>     4283.05824    194.30080      0.00000      7.13336      2.80985
MINI EXTERN>     8424.93723      0.02746      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  12912.26695    115.04720    264.23062      0.00307
STPD INTERN>     4283.05824    194.30080      0.00000      7.13336      2.80985
STPD EXTERN>     8424.93723      0.02746      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2754 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2746 ATOM PAIRS WERE FOUND FOR ATOM LIST
      331 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  12911.16084      1.10611    222.38411      0.00000
MINI INTERN>     4260.10670    202.30333      0.00000      7.14368      2.80100
MINI EXTERN>     8438.77495      0.03118      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2742 ATOM PAIRS WERE FOUND FOR ATOM LIST
      325 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2732 ATOM PAIRS WERE FOUND FOR ATOM LIST
      321 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2743 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2730 ATOM PAIRS WERE FOUND FOR ATOM LIST
      319 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  12246.10483    665.05602    739.40820      0.08265
MINI INTERN>     3492.68141    242.63639      0.00000      5.68547      1.52851
MINI EXTERN>     8504.29244     -0.71939      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40  12031.32542    214.77940     84.99185      0.01399
MINI INTERN>     3460.54245    253.78550      0.00000      5.32857      1.40115
MINI EXTERN>     8311.19912     -0.93137      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2752 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2766 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  11903.34524    127.98018     64.00972      0.02498
MINI INTERN>     3308.36104    310.95220      0.00000      4.63156      0.99487
MINI EXTERN>     8280.31904     -1.91347      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        61
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2774 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        64
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2800 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2772 ATOM PAIRS WERE FOUND FOR ATOM LIST
      331 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        70
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2792 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  11626.96821    276.37703     80.40360      0.02889
MINI INTERN>     2928.73832    326.97966      0.00000      5.71331      1.68741
MINI EXTERN>     8365.92260     -2.07309      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        84
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2812 ATOM PAIRS WERE FOUND FOR ATOM LIST
      334 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        98
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2825 ATOM PAIRS WERE FOUND FOR ATOM LIST
      333 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  11530.84431     96.12390     38.45274      0.01084
MINI INTERN>     2882.37244    312.77382      0.00000      6.45839      1.67811
MINI EXTERN>     8329.66587     -2.10433      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  11512.18345     18.66085     25.93439      0.00407
MINI INTERN>     2887.21929    299.31706      0.00000      7.13492      2.30149
MINI EXTERN>     8318.26777     -2.05708      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  11506.68639      5.49706      8.87881      0.00229
MINI INTERN>     2888.80279    296.48837      0.00000      7.80552      2.34340
MINI EXTERN>     8313.18003     -1.93372      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       142
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2862 ATOM PAIRS WERE FOUND FOR ATOM LIST
      336 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       150
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2882 ATOM PAIRS WERE FOUND FOR ATOM LIST
      343 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  11487.07559     19.61080     34.69821      0.00663
MINI INTERN>     2889.61875    285.47977      0.00000     10.10904      3.57278
MINI EXTERN>     8300.21725     -1.92201      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  11480.03226      7.04333     16.03083      0.00373
MINI INTERN>     2891.79922    280.77004      0.00000     10.31361      3.75018
MINI EXTERN>     8295.22272     -1.82351      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       183
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2900 ATOM PAIRS WERE FOUND FOR ATOM LIST
      338 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200  11473.11399      6.91827     14.15270      0.00311
MINI INTERN>     2887.40070    278.32625      0.00000     10.71314      3.68001
MINI EXTERN>     8294.65586     -1.66197      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  11470.83347      2.28052      4.82080      0.00175
MINI INTERN>     2885.21942    277.25659      0.00000     10.98103      3.29505
MINI EXTERN>     8295.68441     -1.60303      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240  11470.43426      0.39920      7.28262      0.00099
MINI INTERN>     2883.10693    275.53964      0.00000     11.01633      3.24060
MINI EXTERN>     8299.11396     -1.58320      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260  11470.38932      0.04495      1.00538      0.00020
MINI INTERN>     2882.84419    275.51863      0.00000     11.03199      3.23092
MINI EXTERN>     8299.34135     -1.57776      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280  11470.38343      0.00589      0.58207      0.00011
MINI INTERN>     2882.87723    275.55116      0.00000     11.04822      3.21524
MINI EXTERN>     8299.26750     -1.57592      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300  11470.38188      0.00154      0.19491      0.00004
MINI INTERN>     2882.94505    275.47989      0.00000     11.05784      3.20403
MINI EXTERN>     8299.27060     -1.57552      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      310  11470.38149      0.00039      0.06512      0.00006
ABNR INTERN>     2882.96411    275.50011      0.00000     11.06314      3.19684
ABNR EXTERN>     8299.23218     -1.57488      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
 Comparing "11470.4" and "-8.17949".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.485234"
 Parameter: R <- "0.485234"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "11470.4"
Evaluating: 11470.4--8.17949
 Parameter: DELE <- "11478.6"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "11478.6"
Evaluating: 1.00654*11478.6
 Parameter: BETADELE <- "11553.7"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "11553.7"
Evaluating: EXP(-11553.7)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.485234"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.485234".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.485234"
 Comparing "0" and "0.485234".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "4"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "5"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "4"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "4" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.321875"
 Parameter: CHICHOICE1 <- "0.321875"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.321875"
 Parameter: BONDS -> "5"
Evaluating: INT(0.321875*5)
 Parameter: CHICHOICE2 <- "1"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "1"
 Parameter: BONDS -> "5"
 Comparing "1" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "1"
 Parameter: CHICHOICE2 -> "1"
 Comparing "1" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 0.745628
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.774705"
 Parameter: CHI <- "0.774705"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "0.774705"
Evaluating: (0.774705*360)-180.0
 Parameter: CHI1 <- "98.8938"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "98.8938"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI1COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1509 ATOM PAIRS WERE FOUND FOR ATOM LIST
      169 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  32442.92018 -20972.53868  37965.18908      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      8.67289      0.04830
MINI EXTERN>    32412.39238     -0.19045      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1507 ATOM PAIRS WERE FOUND FOR ATOM LIST
      169 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1496 ATOM PAIRS WERE FOUND FOR ATOM LIST
      168 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     98.87215  32344.04803     17.62500      0.02311
MINI INTERN>        6.35947     27.76693      0.00000      7.73165      0.67516
MINI EXTERN>       56.49893     -0.16000      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1472 ATOM PAIRS WERE FOUND FOR ATOM LIST
      169 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     47.65129     51.22086      9.67182      0.01113
MINI INTERN>        1.32457     15.34072      0.00000      7.28744      0.96501
MINI EXTERN>       22.96789     -0.23434      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     31.03164     16.61965      5.46787      0.00536
MINI INTERN>        1.45159     10.62917      0.00000      7.45545      0.77676
MINI EXTERN>       11.02142     -0.30275      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1433 ATOM PAIRS WERE FOUND FOR ATOM LIST
      169 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     23.53283      7.49880      8.55003      0.00619
MINI INTERN>        1.77159      9.05359      0.00000      7.66542      0.64962
MINI EXTERN>        4.73054     -0.33792      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     18.74286      4.78997      2.84217      0.00298
MINI INTERN>        0.74274      8.66590      0.00000      7.82367      0.62455
MINI EXTERN>        1.24176     -0.35576      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     16.01201      2.73085      4.40945      0.00344
MINI INTERN>        0.69982      8.21480      0.00000      7.89400      0.62338
MINI EXTERN>       -1.05410     -0.36587      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     14.00114      2.01088      4.92632      0.00398
MINI INTERN>        0.66601      7.81153      0.00000      7.90107      0.63896
MINI EXTERN>       -2.63761     -0.37882      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     12.20653      1.79461      1.92166      0.00192
MINI INTERN>        0.61448      7.29715      0.00000      7.84105      0.64444
MINI EXTERN>       -3.80279     -0.38781      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       166
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1429 ATOM PAIRS WERE FOUND FOR ATOM LIST
      171 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     10.87645      1.33007      1.59935      0.00221
MINI INTERN>        0.54073      7.00891      0.00000      7.77368      0.66815
MINI EXTERN>       -4.70512     -0.40990      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      9.78508      1.09137      3.41021      0.00256
MINI INTERN>        0.61634      6.70189      0.00000      7.67307      0.68507
MINI EXTERN>       -5.45956     -0.43172      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      9.78508      1.09137      3.41021      0.00128
STPD INTERN>        0.61634      6.70189      0.00000      7.67307      0.68507
STPD EXTERN>       -5.45956     -0.43172      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1429 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1427 ATOM PAIRS WERE FOUND FOR ATOM LIST
      173 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      9.77867      0.00641      1.61588      0.00000
MINI INTERN>        0.44679      6.78606      0.00000      7.69788      0.69678
MINI EXTERN>       -5.41278     -0.43606      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1437 ATOM PAIRS WERE FOUND FOR ATOM LIST
      183 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1472 ATOM PAIRS WERE FOUND FOR ATOM LIST
      190 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -1.16914     10.94781      2.50666      0.01525
MINI INTERN>        0.15075      3.72608      0.00000      6.10408      1.14944
MINI EXTERN>      -11.66109     -0.63839      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1492 ATOM PAIRS WERE FOUND FOR ATOM LIST
      195 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -3.25308      2.08394      1.28749      0.00858
MINI INTERN>        0.08760      2.70908      0.00000      4.97743      0.41381
MINI EXTERN>      -11.37806     -0.06293      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1529 ATOM PAIRS WERE FOUND FOR ATOM LIST
      196 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1563 ATOM PAIRS WERE FOUND FOR ATOM LIST
      205 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        49
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1531 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -4.57378      1.32070      3.71221      0.01636
MINI INTERN>        0.30457      1.67596      0.00000      3.69870      0.28430
MINI EXTERN>      -10.77254      0.23523      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -5.37619      0.80241      0.41617      0.00332
MINI INTERN>        0.11236      1.47996      0.00000      3.73313      0.39083
MINI EXTERN>      -11.15906      0.06660      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        99
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1522 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -5.98648      0.61029      1.10780      0.00518
MINI INTERN>        0.12142      1.37871      0.00000      3.33172      0.34314
MINI EXTERN>      -11.18684      0.02536      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       115
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1491 ATOM PAIRS WERE FOUND FOR ATOM LIST
      187 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -6.49102      0.50454      1.30024      0.00721
MINI INTERN>        0.18176      1.65113      0.00000      2.89057      0.41129
MINI EXTERN>      -11.31634     -0.30944      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -6.88547      0.39444      0.74022      0.00406
MINI INTERN>        0.16882      1.97898      0.00000      2.76265      0.44220
MINI EXTERN>      -11.74003     -0.49808      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       151
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1473 ATOM PAIRS WERE FOUND FOR ATOM LIST
      184 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -7.53535      0.64988      1.23328      0.00634
MINI INTERN>        0.12606      1.68671      0.00000      2.49935      0.30114
MINI EXTERN>      -11.53045     -0.61815      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -7.84573      0.31039      0.63137      0.00357
MINI INTERN>        0.12033      2.05185      0.00000      2.44439      0.45265
MINI EXTERN>      -12.13141     -0.78354      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       192
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1514 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     -8.34854      0.50281      1.07896      0.00558
MINI INTERN>        0.13245      1.56560      0.00000      2.34897      0.34744
MINI EXTERN>      -11.93979     -0.80321      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220     -8.69446      0.34592      0.53089      0.00314
MINI INTERN>        0.13642      1.48316      0.00000      2.20649      0.31129
MINI EXTERN>      -12.07051     -0.76131      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       228
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1533 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      240     -8.89388      0.19943      0.44154      0.00295
MINI INTERN>        0.13287      1.31168      0.00000      2.18307      0.31921
MINI EXTERN>      -12.09229     -0.74842      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -9.00253      0.10864      0.46376      0.00276
MINI INTERN>        0.14554      1.37601      0.00000      2.19920      0.32380
MINI EXTERN>      -12.28809     -0.75899      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       272
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1551 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      280     -9.24476      0.24223      0.52233      0.00259
MINI INTERN>        0.13387      1.37908      0.00000      2.28818      0.37186
MINI EXTERN>      -12.64803     -0.76972      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300     -9.42723      0.18247      0.44125      0.00243
MINI INTERN>        0.13304      1.41965      0.00000      2.19495      0.36806
MINI EXTERN>      -12.83502     -0.70791      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      320     -9.45575      0.02852      0.24589      0.00137
MINI INTERN>        0.12723      1.33615      0.00000      2.20871      0.35735
MINI EXTERN>      -12.76330     -0.72190      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      340     -9.52057      0.06482      0.33304      0.00214
MINI INTERN>        0.12918      1.34094      0.00000      2.21167      0.36370
MINI EXTERN>      -12.83111     -0.73494      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       348
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1623 ATOM PAIRS WERE FOUND FOR ATOM LIST
      191 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      360    -10.17182      0.65125      0.88043      0.00496
MINI INTERN>        0.12614      1.60943      0.00000      2.22473      0.43561
MINI EXTERN>      -13.62386     -0.94387      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      380    -10.39230      0.22048      0.49216      0.00279
MINI INTERN>        0.13748      1.34193      0.00000      2.16493      0.35047
MINI EXTERN>      -13.47704     -0.91007      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      400    -10.50138      0.10908      0.35313      0.00157
MINI INTERN>        0.13032      1.43385      0.00000      2.13408      0.37807
MINI EXTERN>      -13.71310     -0.86460      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      420    -10.61208      0.11070      0.43523      0.00246
MINI INTERN>        0.12714      1.40530      0.00000      2.13625      0.38767
MINI EXTERN>      -13.87700     -0.79144      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       430
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1705 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      440    -10.68978      0.07770      0.41977      0.00230
MINI INTERN>        0.13013      1.38414      0.00000      2.07672      0.34626
MINI EXTERN>      -13.92007     -0.70697      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      460    -10.74425      0.05446      0.13162      0.00078
MINI INTERN>        0.12503      1.46902      0.00000      2.10523      0.37652
MINI EXTERN>      -14.12653     -0.69351      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      465    -10.74840      0.00415      0.08971      0.00069
ABNR INTERN>        0.12543      1.45753      0.00000      2.10157      0.37517
ABNR EXTERN>      -14.11429     -0.69381      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-10.7484"
 Comparing "-10.7484" and "-8.17949".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "-10.7484"
 Comparing "-10.7484" and "-8.17949".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1106.5322  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.890333
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.89033"
 Parameter: RMSD <- "8.89033"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.89033"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.89033" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.89033"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.89033" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.89033"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.89033" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "2"
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    809.5357  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    7.604208
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "7.60421"
 Parameter: RMSD <- "7.60421"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "7.60421"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60421" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "7.60421"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60421" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "7.60421"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60421" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "2"
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-8.17949"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-10.7484"
 Comparing "-10.7484" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-8.17949"
 RDCMND substituted energy or value "?ENER" to "-10.7484"
 Comparing "-10.7484" and "-8.17949".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "7.60421"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "7.60421" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "7.60421"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60421" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "3"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "3"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "3"
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "3"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "3"
 Comparing "3" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "3"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame3.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -10.7484 0.12543 1.45753 2.10157 -14.1143 -0.693815
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-10.7484"
 Parameter: ELAST <- "-10.7484"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "6"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "4"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "4" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.469066"
 Parameter: CHICHOICE1 <- "0.469066"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.469066"
 Parameter: BONDS -> "5"
Evaluating: INT(0.469066*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.587822
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.517668"
 Parameter: CHI <- "0.517668"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.517668"
Evaluating: (0.517668*360)-180.0
 Parameter: CHI2 <- "6.36049"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "6.36049"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3340 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      8.88674      0.04830
MINI EXTERN>  *************     15.84030      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3341 ATOM PAIRS WERE FOUND FOR ATOM LIST
      361 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3351 ATOM PAIRS WERE FOUND FOR ATOM LIST
      379 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3357 ATOM PAIRS WERE FOUND FOR ATOM LIST
      401 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3356 ATOM PAIRS WERE FOUND FOR ATOM LIST
      415 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3349 ATOM PAIRS WERE FOUND FOR ATOM LIST
      406 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3353 ATOM PAIRS WERE FOUND FOR ATOM LIST
      412 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3337 ATOM PAIRS WERE FOUND FOR ATOM LIST
      404 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  38532.60528*************  14004.01796      0.05547
MINI INTERN>     7224.15955    778.64012      0.00000      8.19954      0.52463
MINI EXTERN>    30519.38683      1.69459      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3353 ATOM PAIRS WERE FOUND FOR ATOM LIST
      406 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3345 ATOM PAIRS WERE FOUND FOR ATOM LIST
      405 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        30
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3358 ATOM PAIRS WERE FOUND FOR ATOM LIST
      408 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3370 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  22472.10126  16060.50402   8023.70859      0.06409
MINI INTERN>     6761.30155    560.35422      0.00000      8.38874      5.19792
MINI EXTERN>    15134.45814      2.40069      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3362 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3374 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  16648.42301   5823.67825   1191.49300      0.03086
MINI INTERN>     6107.07660    588.59200      0.00000      8.09934      9.04889
MINI EXTERN>     9933.53409      2.07210      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        68
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3382 ATOM PAIRS WERE FOUND FOR ATOM LIST
      414 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        80
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3382 ATOM PAIRS WERE FOUND FOR ATOM LIST
      407 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  14681.87211   1966.55091    533.74380      0.01486
MINI INTERN>     4983.80517    631.12239      0.00000      8.70194     10.90910
MINI EXTERN>     9045.45512      1.87840      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  14246.66115    435.21096     84.04866      0.00298
MINI INTERN>     4783.06582    615.99493      0.00000      8.85712     11.17334
MINI EXTERN>     8825.92011      1.64982      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  14121.32209    125.33906    137.14298      0.00344
MINI INTERN>     4709.27773    609.92031      0.00000      8.88305     11.50760
MINI EXTERN>     8780.20229      1.53111      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       130
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3369 ATOM PAIRS WERE FOUND FOR ATOM LIST
      395 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  14047.54949     73.77260    164.64080      0.00398
MINI INTERN>     4662.11547    603.19974      0.00000      8.92841     11.78146
MINI EXTERN>     8760.01205      1.51237      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  13985.44411     62.10539    193.19561      0.00460
MINI INTERN>     4621.75532    592.66952      0.00000      9.02743     11.99537
MINI EXTERN>     8748.44241      1.55405      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  13916.65924     68.78486     77.49877      0.00221
MINI INTERN>     4587.44275    576.68794      0.00000      9.18658     12.14630
MINI EXTERN>     8729.56738      1.62829      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  13854.71549     61.94375     68.90072      0.00256
MINI INTERN>     4557.75547    556.45932      0.00000      9.40466     12.25770
MINI EXTERN>     8717.12112      1.71721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  13854.71549     61.94375     68.90072      0.00307
STPD INTERN>     4557.75547    556.45932      0.00000      9.40466     12.25770
STPD EXTERN>     8717.12112      1.71721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3369 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3349 ATOM PAIRS WERE FOUND FOR ATOM LIST
      389 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  13854.71549     61.94375     68.90072      0.00000
MINI INTERN>     4557.75547    556.45932      0.00000      9.40466     12.25770
MINI EXTERN>     8717.12112      1.71721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3300 ATOM PAIRS WERE FOUND FOR ATOM LIST
      379 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  13624.26471    230.45078     92.38270      0.02116
MINI INTERN>     4528.96654    438.90583      0.00000     10.42453     11.63267
MINI EXTERN>     8632.10309      2.23205      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40  13604.86329     19.40142     51.93623      0.00716
MINI INTERN>     4548.41888    431.81472      0.00000     10.07916     11.62812
MINI EXTERN>     8600.87039      2.05202      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3270 ATOM PAIRS WERE FOUND FOR ATOM LIST
      383 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  13598.84883      6.01446     16.03770      0.00242
MINI INTERN>     4554.17535    427.01006      0.00000     10.14112     11.25023
MINI EXTERN>     8594.10063      2.17144      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  13597.94851      0.90032      2.86726      0.00082
MINI INTERN>     4559.76026    424.10801      0.00000     10.29296     11.09067
MINI EXTERN>     8590.53955      2.15706      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  13596.31597      1.63254     13.97061      0.00213
MINI INTERN>     4569.04278    418.16218      0.00000      9.57714     10.73131
MINI EXTERN>     8586.55725      2.24530      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  13595.58963      0.72634      8.24855      0.00120
MINI INTERN>     4562.07466    419.91179      0.00000      8.48056     10.89683
MINI EXTERN>     8591.89778      2.32800      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  13595.45730      0.13232      1.17788      0.00024
MINI INTERN>     4562.33819    422.40910      0.00000      8.27462     10.98352
MINI EXTERN>     8589.11697      2.33491      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  13595.42639      0.03092      1.20900      0.00023
MINI INTERN>     4562.21123    422.23994      0.00000      8.29245     11.00461
MINI EXTERN>     8589.34150      2.33665      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  13595.41187      0.01452      1.16316      0.00021
MINI INTERN>     4561.85472    422.23360      0.00000      8.38044     11.00665
MINI EXTERN>     8589.60524      2.33123      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  13595.40767      0.00420      0.24258      0.00007
MINI INTERN>     4561.23863    422.51504      0.00000      8.40789     11.01459
MINI EXTERN>     8589.89927      2.33225      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      214  13595.40687      0.00080      0.08751      0.00002
ABNR INTERN>     4561.00580    422.63718      0.00000      8.41673     11.01861
ABNR EXTERN>     8589.99692      2.33164      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "13595.4"
 Comparing "13595.4" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "13595.4"
 Comparing "13595.4" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "13595.4"
 Comparing "13595.4" and "-10.7484".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "13595.4"
 Comparing "13595.4" and "-10.7484".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.438785"
 Parameter: R <- "0.438785"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "13595.4"
Evaluating: 13595.4--10.7484
 Parameter: DELE <- "13606.1"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "13606.1"
Evaluating: 1.00654*13606.1
 Parameter: BETADELE <- "13695.1"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "13695.1"
Evaluating: EXP(-13695.1)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.438785"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.438785".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.438785"
 Comparing "0" and "0.438785".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "5"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "7"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "5"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "5" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.661991"
 Parameter: CHICHOICE1 <- "0.661991"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.661991"
 Parameter: BONDS -> "5"
Evaluating: INT(0.661991*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 8.658787E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.282457"
 Parameter: CHI <- "0.282457"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.282457"
Evaluating: (0.282457*360)-180.0
 Parameter: CHI3 <- "-78.3155"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "-78.3155"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2914 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      7.24309      0.04830
MINI EXTERN>  *************      7.67819      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2924 ATOM PAIRS WERE FOUND FOR ATOM LIST
      311 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2943 ATOM PAIRS WERE FOUND FOR ATOM LIST
      332 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20 133212.01449*************  18181.57035      0.00963
MINI INTERN>     2605.31690    310.38405      0.00000      7.68936      3.78100
MINI EXTERN>   130284.89612     -0.05294      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2952 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2950 ATOM PAIRS WERE FOUND FOR ATOM LIST
      366 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2957 ATOM PAIRS WERE FOUND FOR ATOM LIST
      376 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2936 ATOM PAIRS WERE FOUND FOR ATOM LIST
      368 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  36864.73225  96347.28224   2562.53096      0.02670
MINI INTERN>     6499.75692    486.22361      0.00000      9.70363     28.56230
MINI EXTERN>    29841.41450     -0.92871      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2960 ATOM PAIRS WERE FOUND FOR ATOM LIST
      382 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  91.0505 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.6392 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  94.2295 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 105.4421 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 107.3853 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 110.1981 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2978 ATOM PAIRS WERE FOUND FOR ATOM LIST
      382 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 121.6792 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 120.4332 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.0991 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.5361 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0549 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       60  31313.47193   5551.26032    637.70836      0.01286
MINI INTERN>     6086.78893    725.25073      0.00000     10.02698    128.87686
MINI EXTERN>    24363.52215     -0.99372      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.6561 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.9868 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0619 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.8147 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.7978 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5122 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.7842 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.1998 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.2091 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.2337 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.0362 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.9770 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.4406 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.5880 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        75
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2984 ATOM PAIRS WERE FOUND FOR ATOM LIST
      393 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.5038 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.3850 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 134.2731 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.7307 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.8714 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.6969 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       80  28542.33830   2771.13363   1085.66947      0.01486
MINI INTERN>     5487.37877    765.46505      0.00000     11.44347    136.21235
MINI EXTERN>    22142.52601     -0.68735      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.5977 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 134.4298 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.6366 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.4824 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 134.0102 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.2200 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        87
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2992 ATOM PAIRS WERE FOUND FOR ATOM LIST
      398 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 134.7971 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.0327 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.8098 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.9708 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.3606 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 134.4263 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.7331 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.7168 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.7634 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.6713 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.4130 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.3541 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.5422 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.3086 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      100  25891.52598   2650.81232    410.41294      0.00715
MINI INTERN>     5330.11823    811.89131      0.00000     12.35592    133.41198
MINI EXTERN>    19603.67652      0.07203      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.8948 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.5203 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step       103
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3005 ATOM PAIRS WERE FOUND FOR ATOM LIST
      405 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 133.1092 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.2078 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.9929 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.5587 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.9720 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.7924 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.1652 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.1610 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 132.3235 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.7041 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.4553 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.8651 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5883 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.1669 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.6523 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.7651 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.6867 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4829 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      120  25304.64965    586.87633    703.14099      0.00827
MINI INTERN>     5313.40526    832.96933      0.00000     12.77177    129.75885
MINI EXTERN>    19015.08283      0.66161      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.0406 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.3115 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4466 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.8611 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.1245 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5479 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.2100 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.3270 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.3113 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.7771 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5999 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 131.0385 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.6795 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4914 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.8416 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2232 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.9416 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5476 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4021 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.7286 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      140  24988.52128    316.12837    328.58452      0.00398
MINI INTERN>     5263.88039    835.43392      0.00000     12.76469    130.23729
MINI EXTERN>    18745.29896      0.90603      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0840 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.8427 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4341 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2898 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.6567 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.3780 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2573 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4981 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0394 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5939 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8725 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2245 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.3716 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9222 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1784 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2921 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0285 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4248 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8902 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.5079 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      160  24838.04426    150.47702    384.86990      0.00460
MINI INTERN>     5281.45189    837.20340      0.00000     12.60915    129.78084
MINI EXTERN>    18575.98170      1.01728      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1816 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0577 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.3704 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8309 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.4727 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1333 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9867 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.3457 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1105 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9838 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2212 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8335 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2996 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.7007 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9950 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1081 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.7550 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2635 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6356 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9427 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      180  24708.53347    129.51079     89.69087      0.00221
MINI INTERN>     5315.47466    838.85475      0.00000     12.48311    128.63926
MINI EXTERN>    18411.99701      1.08468      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       181
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3020 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0863 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6763 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8998 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0402 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.7663 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.1234 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6668 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.2040 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9227 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8298 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0877 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8949 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8241 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9752 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6679 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0535 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.5587 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.8030 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.9040 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6066 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>      200  24622.24741     86.28606    218.01696      0.00256
MINI INTERN>     5323.20840    837.78980      0.00000     12.41593    127.95305
MINI EXTERN>    18319.76372      1.11652      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  24622.24741     86.28606    218.01696      0.00307
STPD INTERN>     5323.20840    837.78980      0.00000     12.41593    127.95305
STPD EXTERN>    18319.76372      1.11652      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3020 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3021 ATOM PAIRS WERE FOUND FOR ATOM LIST
      414 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6066 MIN=   0.0000 ATOMS:  566  567  568  565
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  24622.24741     86.28606    218.01696      0.00000
MINI INTERN>     5323.20840    837.78980      0.00000     12.41593    127.95305
MINI EXTERN>    18319.76372      1.11652      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 130.0255 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.6268 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3037 ATOM PAIRS WERE FOUND FOR ATOM LIST
      416 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 128.5837 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.5819 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.1055 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 129.5044 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 128.5488 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.5031 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 128.5108 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.7357 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.8391 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.3602 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.0808 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 127.0091 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3061 ATOM PAIRS WERE FOUND FOR ATOM LIST
      410 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.0136 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.6206 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.4972 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.4574 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.9804 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.7035 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       20  24227.92771    394.31970    257.67121      0.02059
MINI INTERN>     5064.00410    807.85013      0.00000     13.04619    126.49067
MINI EXTERN>    18215.51533      1.02128      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.2743 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.9935 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 126.2827 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.8920 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.9508 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.9434 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.4569 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.3214 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.2921 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 125.1988 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 124.6839 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 124.4745 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 123.6788 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 122.1871 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 118.0022 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3076 ATOM PAIRS WERE FOUND FOR ATOM LIST
      427 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 102.2957 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3076 ATOM PAIRS WERE FOUND FOR ATOM LIST
      419 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 117.6011 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 116.3319 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 113.2456 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 110.1838 MIN=   0.0000 ATOMS:  566  567  568  565
MINI>       40  24026.82353    201.10418    166.60454      0.01908
MINI INTERN>     5171.29318    740.11266      0.00000     14.20903     98.25687
MINI EXTERN>    18002.43505      0.51674      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 104.3860 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI= 104.9303 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3021 ATOM PAIRS WERE FOUND FOR ATOM LIST
      433 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  89.2014 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  86.3383 MIN=   0.0000 ATOMS:  566  567  568  565
 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  92.5570 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        46
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3026 ATOM PAIRS WERE FOUND FOR ATOM LIST
      439 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3029 ATOM PAIRS WERE FOUND FOR ATOM LIST
      433 GROUP PAIRS REQUIRED ATOM SEARCHES

 EPHI: WARNING. bent improper torsion angle is 

far from minimum for;
    IPHI=    2  with deltaPHI=  85.7846 MIN=   0.0000 ATOMS:  566  567  568  565
 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3020 ATOM PAIRS WERE FOUND FOR ATOM LIST
      437 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3007 ATOM PAIRS WERE FOUND FOR ATOM LIST
      423 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  22246.91538   1779.90814    490.45399      0.09977
MINI INTERN>     6098.92412    478.08020      0.00000     12.38250     20.58954
MINI EXTERN>    15635.00129      1.93774      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        61
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3026 ATOM PAIRS WERE FOUND FOR ATOM LIST
      425 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        62
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3011 ATOM PAIRS WERE FOUND FOR ATOM LIST
      427 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        73
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2998 ATOM PAIRS WERE FOUND FOR ATOM LIST
      422 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  21768.06316    478.85222    162.77744      0.01849
MINI INTERN>     5790.81992    496.43187      0.00000     13.17940     21.72915
MINI EXTERN>    15444.45310      1.44973      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        87
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2985 ATOM PAIRS WERE FOUND FOR ATOM LIST
      428 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        90
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2968 ATOM PAIRS WERE FOUND FOR ATOM LIST
      430 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        92
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2988 ATOM PAIRS WERE FOUND FOR ATOM LIST
      427 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        93
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2968 ATOM PAIRS WERE FOUND FOR ATOM LIST
      430 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       100
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2959 ATOM PAIRS WERE FOUND FOR ATOM LIST
      430 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  21587.77406    180.28911    203.69664      0.01903
MINI INTERN>     5992.69653    462.72849      0.00000     11.35317     23.53667
MINI EXTERN>    15096.58525      0.87396      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       104
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2961 ATOM PAIRS WERE FOUND FOR ATOM LIST
      428 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       107
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2961 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       114
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2950 ATOM PAIRS WERE FOUND FOR ATOM LIST
      413 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  21055.76854    532.00551    107.36609      0.01785
MINI INTERN>     5454.21820    500.37694      0.00000     10.34898     19.11805
MINI EXTERN>    15070.35954      1.34682      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  21023.44439     32.32415     27.20239      0.00286
MINI INTERN>     5448.14872    491.31317      0.00000     10.69996     18.91876
MINI EXTERN>    15053.06437      1.29941      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  21021.93575      1.50864     18.29452      0.00161
MINI INTERN>     5443.28233    488.47431      0.00000     10.78490     18.76660
MINI EXTERN>    15059.32513      1.30247      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  21021.68111      0.25464      3.04494      0.00033
MINI INTERN>     5446.69102    488.32538      0.00000     10.83893     18.67708
MINI EXTERN>    15055.84631      1.30240      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  21021.58196      0.09914      3.46324      0.00031
MINI INTERN>     5446.29237    489.05188      0.00000     10.88694     18.61973
MINI EXTERN>    15055.42672      1.30431      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  21021.57169      0.01027      0.87543      0.00010
MINI INTERN>     5445.61903    489.02409      0.00000     10.89072     18.63419
MINI EXTERN>    15056.09912      1.30454      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      239  21021.57106      0.00063      0.09492      0.00002
ABNR INTERN>     5445.68480    488.98731      0.00000     10.89092     18.63236
ABNR EXTERN>    15056.07076      1.30490      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "21021.6"
 Comparing "21021.6" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "21021.6"
 Comparing "21021.6" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "21021.6"
 Comparing "21021.6" and "-10.7484".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "21021.6"
 Comparing "21021.6" and "-10.7484".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.262496"
 Parameter: R <- "0.262496"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "21021.6"
Evaluating: 21021.6--10.7484
 Parameter: DELE <- "21032.3"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "21032.3"
Evaluating: 1.00654*21032.3
 Parameter: BETADELE <- "21169.9"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "21169.9"
Evaluating: EXP(-21169.9)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.262496"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.262496".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.262496"
 Comparing "0" and "0.262496".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "6"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "8"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "6"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "6" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.776749"
 Parameter: CHICHOICE1 <- "0.776749"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.776749"
 Parameter: BONDS -> "5"
Evaluating: INT(0.776749*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.821794
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.898972"
 Parameter: CHI <- "0.898972"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.898972"
Evaluating: (0.898972*360)-180.0
 Parameter: CHI3 <- "143.63"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "143.63"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2484 ATOM PAIRS WERE FOUND FOR ATOM LIST
      280 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0 202049.58494-181028.01388 160739.04480      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     12.10180      0.04830
MINI EXTERN>   202013.68071      1.75708      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2463 ATOM PAIRS WERE FOUND FOR ATOM LIST
      264 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2430 ATOM PAIRS WERE FOUND FOR ATOM LIST
      240 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2346 ATOM PAIRS WERE FOUND FOR ATOM LIST
      233 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    251.90730 201797.67764     74.93168      0.05547
MINI INTERN>       67.56667    100.80731      0.00000      4.55072      1.21749
MINI EXTERN>       78.07542     -0.31030      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2287 ATOM PAIRS WERE FOUND FOR ATOM LIST
      240 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2207 ATOM PAIRS WERE FOUND FOR ATOM LIST
      241 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     60.99098    190.91633     10.13359      0.01113
MINI INTERN>        7.43467     21.37675      0.00000      4.32421      2.01290
MINI EXTERN>       26.10294     -0.26049      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        55
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2166 ATOM PAIRS WERE FOUND FOR ATOM LIST
      238 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     30.55485     30.43613     17.41494      0.01286
MINI INTERN>        3.93728     12.00920      0.00000      3.93631      1.72176
MINI EXTERN>        9.33562     -0.38532      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     15.46001     15.09484      5.51365      0.00619
MINI INTERN>        1.13520      9.30280      0.00000      3.69511      1.27695
MINI EXTERN>        0.55276     -0.50282      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        94
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2107 ATOM PAIRS WERE FOUND FOR ATOM LIST
      244 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     10.33444      5.12557      9.49074      0.00715
MINI INTERN>        1.27200      8.63265      0.00000      3.52275      0.99113
MINI EXTERN>       -3.46683     -0.61727      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      6.23780      4.09664      2.62183      0.00344
MINI INTERN>        0.46605      8.02174      0.00000      3.39687      0.83319
MINI EXTERN>       -5.77956     -0.70050      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      4.11704      2.12076      4.98093      0.00398
MINI INTERN>        0.56107      7.55944      0.00000      3.28776      0.71613
MINI EXTERN>       -7.26659     -0.74076      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160      2.29063      1.82640      1.99027      0.00192
MINI INTERN>        0.39298      7.14703      0.00000      3.17631      0.59720
MINI EXTERN>       -8.26283     -0.76005      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180      1.00255      1.28808      1.60977      0.00221
MINI INTERN>        0.35989      6.77808      0.00000      3.09002      0.53214
MINI EXTERN>       -8.99726     -0.76031      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      0.02073      0.98182      3.65476      0.00256
MINI INTERN>        0.44070      6.43541      0.00000      3.00183      0.47422
MINI EXTERN>       -9.57958     -0.75185      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      0.02073      0.98182      3.65476      0.00128
STPD INTERN>        0.44070      6.43541      0.00000      3.00183      0.47422
STPD EXTERN>       -9.57958     -0.75185      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2107 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2064 ATOM PAIRS WERE FOUND FOR ATOM LIST
      239 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -0.00624      0.02697      1.81405      0.00000
MINI INTERN>        0.33812      6.44652      0.00000      3.01857      0.49450
MINI EXTERN>       -9.55398     -0.74997      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1963 ATOM PAIRS WERE FOUND FOR ATOM LIST
      239 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -8.25711      8.25087      4.26996      0.01830
MINI INTERN>        0.35333      2.30465      0.00000      2.16510      0.17795
MINI EXTERN>      -12.49564     -0.76250      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1928 ATOM PAIRS WERE FOUND FOR ATOM LIST
      231 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -8.81160      0.55449      1.34351      0.00618
MINI INTERN>        0.23758      2.07527      0.00000      2.21529      0.21629
MINI EXTERN>      -12.88809     -0.66794      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -9.16655      0.35495      0.66018      0.00348
MINI INTERN>        0.15648      1.89133      0.00000      2.30231      0.31680
MINI EXTERN>      -12.95375     -0.87971      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -9.22426      0.05771      0.24652      0.00117
MINI INTERN>        0.16800      2.01702      0.00000      2.40196      0.33486
MINI EXTERN>      -13.24524     -0.90087      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>       90     -9.23186      0.00760      0.09311      0.00102
ABNR INTERN>        0.16808      2.00770      0.00000      2.39606      0.33236
ABNR EXTERN>      -13.25197     -0.88408      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-9.23186"
 Comparing "-9.23186" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "-9.23186"
 Comparing "-9.23186" and "-10.7484".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-10.7484"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-9.23186"
 Comparing "-9.23186" and "-10.7484".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "-9.23186"
 Comparing "-9.23186" and "-10.7484".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "2.788159E-02"
 Parameter: R <- "2.788159E-02"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-10.7484"
 RDCMND substituted energy or value "?ENER" to "-9.23186"
Evaluating: -9.23186--10.7484
 Parameter: DELE <- "1.51654"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "1.51654"
Evaluating: 1.00654*1.51654
 Parameter: BETADELE <- "1.52646"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "1.52646"
Evaluating: EXP(-1.52646)
 Parameter: DELN <- "0.217304"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.217304"
 Parameter: R -> "2.788159E-02"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.217304" and "2.788159E-02".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.217304"
 Parameter: R -> "2.788159E-02"
 Comparing "0.217304" and "2.788159E-02".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.217304"
 Parameter: R -> "2.788159E-02"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.217304" and "2.788159E-02".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.217304"
 Parameter: R -> "2.788159E-02"
 Comparing "0.217304" and "2.788159E-02".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1042.0990  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.627609
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.62761"
 Parameter: RMSD <- "8.62761"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.62761"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.62761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.62761"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.62761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.62761"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.62761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "3"
 Comparing "2" and "3".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    746.8364  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    7.303797
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "7.3038"
 Parameter: RMSD <- "7.3038"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "7.3038"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.3038" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "7.3038"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.3038" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "7.3038"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.3038" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "3"
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    188.9887  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.674125
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.67413"
 Parameter: RMSD <- "3.67413"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.67413"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.67413" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.67413"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.67413" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.67413"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.67413" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "3"
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "3.67413"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3.67413" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "3.67413"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.67413" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "4"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "4"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "4"
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "4"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "4" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "4"
 Comparing "4" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "4"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame4.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -9.23186 0.168075 2.0077 2.39606 -13.252 -0.884084
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-9.23186"
 Parameter: ELAST <- "-9.23186"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "9"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "6"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "6" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.605894"
 Parameter: CHICHOICE1 <- "0.605894"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.605894"
 Parameter: BONDS -> "5"
Evaluating: INT(0.605894*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.264897
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.123811"
 Parameter: CHI <- "0.123811"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.123811"
Evaluating: (0.123811*360)-180.0
 Parameter: CHI3 <- "-135.428"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "-135.428"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3372 ATOM PAIRS WERE FOUND FOR ATOM LIST
      348 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.97473      0.04830
MINI EXTERN>  *************      7.57549      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3376 ATOM PAIRS WERE FOUND FOR ATOM LIST
      348 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3390 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3408 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3435 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3435 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3419 ATOM PAIRS WERE FOUND FOR ATOM LIST
      354 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  11123.97699*************   3913.79437      0.05547
MINI INTERN>     2086.12505    418.09849      0.00000      9.01503      1.35435
MINI EXTERN>     8606.90829      2.47578      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        39
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3445 ATOM PAIRS WERE FOUND FOR ATOM LIST
      349 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   7426.75645   3697.22054    522.77171      0.01113
MINI INTERN>     1654.33449    358.30786      0.00000      9.01726      0.83618
MINI EXTERN>     5402.55401      1.70666      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60   7006.10872    420.64773    106.19786      0.00536
MINI INTERN>     1541.04559    295.56649      0.00000      8.97341      1.83806
MINI EXTERN>     5157.34640      1.33878      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80   6789.42530    216.68342    269.75812      0.00619
MINI INTERN>     1430.11631    262.08774      0.00000      8.97247      2.13834
MINI EXTERN>     5085.09152      1.01891      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        93
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3467 ATOM PAIRS WERE FOUND FOR ATOM LIST
      359 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   6609.29210    180.13320     81.76583      0.00298
MINI INTERN>     1351.07933    266.41477      0.00000      8.99451      1.86547
MINI EXTERN>     4980.18182      0.75620      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120   6463.86283    145.42927     78.70614      0.00344
MINI INTERN>     1252.38564    290.57850      0.00000      8.98936      1.40096
MINI EXTERN>     4909.98812      0.52025      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140   6336.90658    126.95625     99.29541      0.00398
MINI INTERN>     1166.72208    320.45728      0.00000      8.91424      0.95075
MINI EXTERN>     4839.53548      0.32674      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       149
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3486 ATOM PAIRS WERE FOUND FOR ATOM LIST
      363 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160   6240.55036     96.35622    199.75483      0.00460
MINI INTERN>     1107.07476    344.66796      0.00000      8.76054      0.61840
MINI EXTERN>     4779.25664      0.17207      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   6146.60370     93.94666     72.97835      0.00221
MINI INTERN>     1040.93714    360.65366      0.00000      8.53819      0.40053
MINI EXTERN>     4736.03150      0.04267      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200   6084.23704     62.36666     68.44035      0.00256
MINI INTERN>     1007.05863    369.25550      0.00000      8.28748      0.28423
MINI EXTERN>     4699.41518     -0.06398      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   6084.23704     62.36666     68.44035      0.00307
STPD INTERN>     1007.05863    369.25550      0.00000      8.28748      0.28423
STPD EXTERN>     4699.41518     -0.06398      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3486 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3494 ATOM PAIRS WERE FOUND FOR ATOM LIST
      374 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   6084.23704     62.36666     68.44035      0.00000
MINI INTERN>     1007.05863    369.25550      0.00000      8.28748      0.28423
MINI EXTERN>     4699.41518     -0.06398      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3526 ATOM PAIRS WERE FOUND FOR ATOM LIST
      382 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3574 ATOM PAIRS WERE FOUND FOR ATOM LIST
      385 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   5906.90259    177.33444    471.10756      0.04463
MINI INTERN>      869.19533    384.92103      0.00000      4.63623      0.24768
MINI EXTERN>     4647.95068     -0.04835      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40   5828.41072     78.49187     39.08645      0.01377
MINI INTERN>      816.97180    337.84772      0.00000      5.21090      0.54159
MINI EXTERN>     4667.72334      0.11537      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3617 ATOM PAIRS WERE FOUND FOR ATOM LIST
      386 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   5824.98662      3.42410     10.12625      0.00280
MINI INTERN>      814.58631    338.78417      0.00000      5.61390      0.71219
MINI EXTERN>     4665.05212      0.23793      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80   5824.82047      0.16615      2.60895      0.00057
MINI INTERN>      815.38774    340.06824      0.00000      5.64723      0.64157
MINI EXTERN>     4662.85227      0.22342      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100   5824.81091      0.00956      0.49854      0.00011
MINI INTERN>      815.63160    340.23433      0.00000      5.66735      0.62331
MINI EXTERN>     4662.43465      0.21966      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      105   5824.81070      0.00021      0.08701      0.00006
ABNR INTERN>      815.66655    340.21607      0.00000      5.66887      0.62271
ABNR EXTERN>     4662.41713      0.21938      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "5824.81"
 Comparing "5824.81" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "5824.81"
 Comparing "5824.81" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "5824.81"
 Comparing "5824.81" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "5824.81"
 Comparing "5824.81" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.897951"
 Parameter: R <- "0.897951"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "5824.81"
Evaluating: 5824.81--9.23186
 Parameter: DELE <- "5834.04"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "5834.04"
Evaluating: 1.00654*5834.04
 Parameter: BETADELE <- "5872.19"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "5872.19"
Evaluating: EXP(-5872.19)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.897951"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.897951".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.897951"
 Comparing "0" and "0.897951".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "7"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "10"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "7"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "7" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.859535"
 Parameter: CHICHOICE1 <- "0.859535"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.859535"
 Parameter: BONDS -> "5"
Evaluating: INT(0.859535*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.210783
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.627443"
 Parameter: CHI <- "0.627443"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.627443"
Evaluating: (0.627443*360)-180.0
 Parameter: CHI4 <- "45.8795"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "45.8795"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3221 ATOM PAIRS WERE FOUND FOR ATOM LIST
      346 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     11.74313      0.04830
MINI EXTERN>  *************      2.47923      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3228 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3238 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3238 ATOM PAIRS WERE FOUND FOR ATOM LIST
      359 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3255 ATOM PAIRS WERE FOUND FOR ATOM LIST
      359 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3267 ATOM PAIRS WERE FOUND FOR ATOM LIST
      359 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3255 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  19349.36337*************   3009.28657      0.02311
MINI INTERN>     3738.17546    592.69161      0.00000     10.43462      2.09389
MINI EXTERN>    15006.98019     -1.01239      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        30
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3251 ATOM PAIRS WERE FOUND FOR ATOM LIST
      359 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        34
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3245 ATOM PAIRS WERE FOUND FOR ATOM LIST
      363 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3239 ATOM PAIRS WERE FOUND FOR ATOM LIST
      363 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   9175.24381  10174.11956   1056.11425      0.06409
MINI INTERN>     4329.62530    616.09414      0.00000     11.08138      1.22318
MINI EXTERN>     4217.68698     -0.46718      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3239 ATOM PAIRS WERE FOUND FOR ATOM LIST
      370 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3229 ATOM PAIRS WERE FOUND FOR ATOM LIST
      365 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        46
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3234 ATOM PAIRS WERE FOUND FOR ATOM LIST
      369 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3231 ATOM PAIRS WERE FOUND FOR ATOM LIST
      360 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3234 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   6758.88901   2416.35481    274.10282      0.03086
MINI INTERN>     4116.41903    601.24423      0.00000     10.88538      1.50220
MINI EXTERN>     2028.75209      0.08607      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        67
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3223 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        78
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3221 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   6090.18699    668.70202    241.97673      0.03566
MINI INTERN>     3648.08538    531.12034      0.00000     10.54957      2.73833
MINI EXTERN>     1897.62220      0.07117      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100   5787.17682    303.01017     56.85423      0.00715
MINI INTERN>     3352.17191    445.53663      0.00000     10.43359      4.31008
MINI EXTERN>     1974.45926      0.26534      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       110
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3217 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120   5730.87056     56.30626     67.71146      0.00827
MINI INTERN>     3370.29959    409.50097      0.00000     10.19288      5.19651
MINI EXTERN>     1935.29773      0.38288      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140   5698.35844     32.51212     32.87656      0.00398
MINI INTERN>     3270.45185    381.20002      0.00000      9.97005      5.87778
MINI EXTERN>     2030.41397      0.44478      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160   5684.94215     13.41629     39.57991      0.00460
MINI INTERN>     3261.82843    368.00160      0.00000      9.80744      6.06786
MINI EXTERN>     2038.76289      0.47392      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       163
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3216 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180   5674.77658     10.16557     10.38348      0.00221
MINI INTERN>     3304.43740    362.59071      0.00000      9.67801      5.99395
MINI EXTERN>     1991.57425      0.50226      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200   5669.23772      5.53885     21.04414      0.00256
MINI INTERN>     3315.73454    357.41787      0.00000      9.56435      5.95543
MINI EXTERN>     1980.02104      0.54450      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   5669.23772      5.53885     21.04414      0.00307
STPD INTERN>     3315.73454    357.41787      0.00000      9.56435      5.95543
STPD EXTERN>     1980.02104      0.54450      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3216 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3228 ATOM PAIRS WERE FOUND FOR ATOM LIST
      358 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   5669.23772      5.53885     21.04414      0.00000
MINI INTERN>     3315.73454    357.41787      0.00000      9.56435      5.95543
MINI EXTERN>     1980.02104      0.54450      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3256 ATOM PAIRS WERE FOUND FOR ATOM LIST
      361 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   5642.31828     26.91945      6.83923      0.00988
MINI INTERN>     3268.78272    336.62818      0.00000      8.73109      6.99393
MINI EXTERN>     2020.04958      1.13278      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3336 ATOM PAIRS WERE FOUND FOR ATOM LIST
      366 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3404 ATOM PAIRS WERE FOUND FOR ATOM LIST
      370 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3354 ATOM PAIRS WERE FOUND FOR ATOM LIST
      362 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3338 ATOM PAIRS WERE FOUND FOR ATOM LIST
      354 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        33
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3359 ATOM PAIRS WERE FOUND FOR ATOM LIST
      346 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3349 ATOM PAIRS WERE FOUND FOR ATOM LIST
      344 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3349 ATOM PAIRS WERE FOUND FOR ATOM LIST
      345 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3356 ATOM PAIRS WERE FOUND FOR ATOM LIST
      345 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   4360.34254   1281.97574    244.52681      0.60573
MINI INTERN>     1582.02718    650.54761      0.00000      8.85023      0.07521
MINI EXTERN>     2117.09178      1.75054      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3379 ATOM PAIRS WERE FOUND FOR ATOM LIST
      372 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3390 ATOM PAIRS WERE FOUND FOR ATOM LIST
      394 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3379 ATOM PAIRS WERE FOUND FOR ATOM LIST
      367 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        46
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3417 ATOM PAIRS WERE FOUND FOR ATOM LIST
      393 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3402 ATOM PAIRS WERE FOUND FOR ATOM LIST
      373 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3473 ATOM PAIRS WERE FOUND FOR ATOM LIST
      390 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        54
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3499 ATOM PAIRS WERE FOUND FOR ATOM LIST
      395 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3574 ATOM PAIRS WERE FOUND FOR ATOM LIST
      405 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   2823.48320   1536.85933     53.13569      0.20762
MINI INTERN>      721.67572    451.87129      0.00000      5.68238      0.86675
MINI EXTERN>     1643.18476      0.20230      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        70
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3616 ATOM PAIRS WERE FOUND FOR ATOM LIST
      410 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   2760.57308     62.91012     11.04337      0.02244
MINI INTERN>      644.07795    420.83332      0.00000      5.87722      2.17030
MINI EXTERN>     1687.21722      0.39706      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100   2759.65586      0.91722      0.97676      0.00273
MINI INTERN>      645.90578    421.94966      0.00000      5.91710      2.02654
MINI EXTERN>     1683.43805      0.41873      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120   2759.63088      0.02498      0.12718      0.00033
MINI INTERN>      645.51398    421.85375      0.00000      5.87269      2.05343
MINI EXTERN>     1683.91844      0.41860      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      125   2759.63080      0.00008      0.07345      0.00018
ABNR INTERN>      645.54764    421.87497      0.00000      5.87254      2.05237
ABNR EXTERN>     1683.86470      0.41858      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "2759.63"
 Comparing "2759.63" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "2759.63"
 Comparing "2759.63" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "2759.63"
 Comparing "2759.63" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "2759.63"
 Comparing "2759.63" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.427317"
 Parameter: R <- "0.427317"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "2759.63"
Evaluating: 2759.63--9.23186
 Parameter: DELE <- "2768.86"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "2768.86"
Evaluating: 1.00654*2768.86
 Parameter: BETADELE <- "2786.97"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "2786.97"
Evaluating: EXP(-2786.97)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.427317"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.427317".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.427317"
 Comparing "0" and "0.427317".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "8"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "11"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "8"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "8" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.916533"
 Parameter: CHICHOICE1 <- "0.916533"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.916533"
 Parameter: BONDS -> "5"
Evaluating: INT(0.916533*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.16461
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.600245"
 Parameter: CHI <- "0.600245"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.600245"
Evaluating: (0.600245*360)-180.0
 Parameter: CHI4 <- "36.0882"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "36.0882"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3148 ATOM PAIRS WERE FOUND FOR ATOM LIST
      342 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     12.14727      0.04830
MINI EXTERN>  *************      1.75991      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3149 ATOM PAIRS WERE FOUND FOR ATOM LIST
      343 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3123 ATOM PAIRS WERE FOUND FOR ATOM LIST
      357 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3121 ATOM PAIRS WERE FOUND FOR ATOM LIST
      370 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3102 ATOM PAIRS WERE FOUND FOR ATOM LIST
      378 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3096 ATOM PAIRS WERE FOUND FOR ATOM LIST
      370 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3078 ATOM PAIRS WERE FOUND FOR ATOM LIST
      368 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  20870.62458*************  17760.62968      0.13312
MINI INTERN>     2590.02569    354.42832      0.00000     10.88689      1.77295
MINI EXTERN>    17913.32103      0.18970      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3079 ATOM PAIRS WERE FOUND FOR ATOM LIST
      372 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3068 ATOM PAIRS WERE FOUND FOR ATOM LIST
      365 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3040 ATOM PAIRS WERE FOUND FOR ATOM LIST
      361 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   4272.11152  16598.51306    101.58523      0.02670
MINI INTERN>     2474.49505    294.12992      0.00000     11.30743      0.73025
MINI EXTERN>     1492.51711     -1.06824      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3025 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        54
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3032 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   3650.19155    621.91997    123.76354      0.03086
MINI INTERN>     2137.59869    285.61221      0.00000     11.58539      2.79245
MINI EXTERN>     1213.90061     -1.29782      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        66
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3042 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   3396.14877    254.04278     60.52333      0.01486
MINI INTERN>     1775.40514    264.21111      0.00000     10.57286      4.41183
MINI EXTERN>     1342.24280     -0.69497      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        81
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3056 ATOM PAIRS WERE FOUND FOR ATOM LIST
      357 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   3328.28498     67.86379     26.35094      0.00715
MINI INTERN>     1830.47181    259.09218      0.00000      9.47286      3.68659
MINI EXTERN>     1225.84249     -0.28095      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120   3300.83186     27.45312      7.72569      0.00344
MINI INTERN>     1780.90710    252.59231      0.00000      8.40707      4.22163
MINI EXTERN>     1254.68183      0.02192      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       125
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3081 ATOM PAIRS WERE FOUND FOR ATOM LIST
      361 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140   3287.54597     13.28589     10.37823      0.00398
MINI INTERN>     1760.75446    250.76655      0.00000      7.86904      4.84726
MINI EXTERN>     1263.05685      0.25180      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160   3281.29805      6.24792      4.00493      0.00192
MINI INTERN>     1769.74916    251.32337      0.00000      7.79942      5.13928
MINI EXTERN>     1246.91924      0.36758      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   3277.90142      3.39663      7.89035      0.00221
MINI INTERN>     1775.34691    252.18799      0.00000      7.88065      5.33376
MINI EXTERN>     1236.71727      0.43484      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200   3276.00487      1.89655      2.90040      0.00107
MINI INTERN>     1760.69099    252.26891      0.00000      7.98052      5.52999
MINI EXTERN>     1249.07118      0.46328      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   3276.00487      1.89655      2.90040      0.00128
STPD INTERN>     1760.69099    252.26891      0.00000      7.98052      5.52999
STPD EXTERN>     1249.07118      0.46328      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3081 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3090 ATOM PAIRS WERE FOUND FOR ATOM LIST
      360 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   3276.00487      1.89655      2.90040      0.00000
MINI INTERN>     1760.69099    252.26891      0.00000      7.98052      5.52999
MINI EXTERN>     1249.07118      0.46328      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20   3274.07507      1.92980      1.11932      0.00278
MINI INTERN>     1761.61853    254.96514      0.00000      8.33362      5.70781
MINI EXTERN>     1243.01111      0.43886      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40   3274.06720      0.00787      0.13719      0.00034
MINI INTERN>     1760.66577    254.95853      0.00000      8.33104      5.71186
MINI EXTERN>     1243.95981      0.44018      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>       41   3274.06716      0.00004      0.09678      0.00027
ABNR INTERN>     1760.74068    255.01119      0.00000      8.33088      5.70944
ABNR EXTERN>     1243.83478      0.44019      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "3274.07"
 Comparing "3274.07" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3274.07"
 Comparing "3274.07" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "3274.07"
 Comparing "3274.07" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3274.07"
 Comparing "3274.07" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.325826"
 Parameter: R <- "0.325826"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3274.07"
Evaluating: 3274.07--9.23186
 Parameter: DELE <- "3283.3"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "3283.3"
Evaluating: 1.00654*3283.3
 Parameter: BETADELE <- "3304.77"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "3304.77"
Evaluating: EXP(-3304.77)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.325826"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.325826".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.325826"
 Comparing "0" and "0.325826".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "9"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "12"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "9"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "9" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.149468"
 Parameter: CHICHOICE1 <- "0.149468"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.149468"
 Parameter: BONDS -> "5"
Evaluating: INT(0.149468*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.10658
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.298316"
 Parameter: CHI <- "0.298316"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.298316"
Evaluating: (0.298316*360)-180.0
 Parameter: CHI5 <- "-72.6062"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "-72.6062"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2877 ATOM PAIRS WERE FOUND FOR ATOM LIST
      314 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     12.14727      0.04830
MINI EXTERN>  *************     20.51747      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2873 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2869 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2851 ATOM PAIRS WERE FOUND FOR ATOM LIST
      321 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2832 ATOM PAIRS WERE FOUND FOR ATOM LIST
      321 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  84595.79563*************  31182.76216      0.05547
MINI INTERN>     3361.77878    367.29771      0.00000     10.94504      0.96375
MINI EXTERN>    80857.26436     -2.45402      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2824 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2804 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2793 ATOM PAIRS WERE FOUND FOR ATOM LIST
      312 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        27
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2798 ATOM PAIRS WERE FOUND FOR ATOM LIST
      312 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2783 ATOM PAIRS WERE FOUND FOR ATOM LIST
      312 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2782 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        30
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2781 ATOM PAIRS WERE FOUND FOR ATOM LIST
      315 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        33
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2762 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  15857.31325  68738.48238    276.91145      0.01113
MINI INTERN>     5836.31059    847.02020      0.00000      9.02891      1.85950
MINI EXTERN>     9165.36392     -2.26986      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60  14848.80633   1008.50692    443.33147      0.01286
MINI INTERN>     5541.11275    859.08505      0.00000      8.99724      2.80597
MINI EXTERN>     8439.01670     -2.21139      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        63
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2678 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  14341.42835    507.37798    122.21965      0.00619
MINI INTERN>     5383.56942    822.70621      0.00000      8.94020      3.26666
MINI EXTERN>     8125.07596     -2.13010      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        94
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2651 ATOM PAIRS WERE FOUND FOR ATOM LIST
      307 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  13926.89161    414.53674    216.77082      0.00715
MINI INTERN>     5185.40098    745.03629      0.00000      8.39939      3.65421
MINI EXTERN>     7986.31879     -1.91805      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       117
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2620 ATOM PAIRS WERE FOUND FOR ATOM LIST
      303 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  13447.91928    478.97233    146.53824      0.00827
MINI INTERN>     4881.40324    673.02001      0.00000      7.30660      3.97055
MINI EXTERN>     7883.93632     -1.71745      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       137
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2580 ATOM PAIRS WERE FOUND FOR ATOM LIST
      300 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  12908.04898    539.87030    321.63306      0.00955
MINI INTERN>     4435.48918    670.94751      0.00000      7.42594      4.30880
MINI EXTERN>     7791.44484     -1.56729      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       157
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2560 ATOM PAIRS WERE FOUND FOR ATOM LIST
      298 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  12378.58519    529.46379    373.10089      0.01104
MINI INTERN>     3989.47047    710.24800      0.00000      8.48016      4.73157
MINI EXTERN>     7667.06854     -1.41354      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       179
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2546 ATOM PAIRS WERE FOUND FOR ATOM LIST
      300 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180  11934.35237    444.23282    420.89307      0.01275
MINI INTERN>     3647.53901    727.73987      0.00000      8.61152      5.63554
MINI EXTERN>     7546.10831     -1.28189      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  11549.43442    384.91795    489.67021      0.01474
MINI INTERN>     3371.24222    744.45209      0.00000      8.35042      6.82569
MINI EXTERN>     7419.83184     -1.26783      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  11549.43442    384.91795    489.67021      0.00737
STPD INTERN>     3371.24222    744.45209      0.00000      8.35042      6.82569
STPD EXTERN>     7419.83184     -1.26783      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2546 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2541 ATOM PAIRS WERE FOUND FOR ATOM LIST
      293 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  11542.78100      6.65342    442.90113      0.00000
MINI INTERN>     3363.64443    740.19425      0.00000      8.36261      6.77361
MINI EXTERN>     7425.07383     -1.26772      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2522 ATOM PAIRS WERE FOUND FOR ATOM LIST
      286 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2490 ATOM PAIRS WERE FOUND FOR ATOM LIST
      281 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  10448.96494   1093.81606    456.76158      0.08707
MINI INTERN>     2464.99509    805.99823      0.00000      7.71609     10.93784
MINI EXTERN>     7160.56909     -1.25139      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2445 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2404 ATOM PAIRS WERE FOUND FOR ATOM LIST
      266 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2331 ATOM PAIRS WERE FOUND FOR ATOM LIST
      261 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        34
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2273 ATOM PAIRS WERE FOUND FOR ATOM LIST
      257 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2244 ATOM PAIRS WERE FOUND FOR ATOM LIST
      250 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2272 ATOM PAIRS WERE FOUND FOR ATOM LIST
      256 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2231 ATOM PAIRS WERE FOUND FOR ATOM LIST
      249 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2256 ATOM PAIRS WERE FOUND FOR ATOM LIST
      253 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        40
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2216 ATOM PAIRS WERE FOUND FOR ATOM LIST
      244 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   9370.14797   1078.81697    267.97624      0.08067
MINI INTERN>     1599.28982    996.98606      0.00000      7.21666     25.72860
MINI EXTERN>     6741.66525     -0.73842      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        59
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2180 ATOM PAIRS WERE FOUND FOR ATOM LIST
      233 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   9078.22511    291.92286    251.75979      0.04552
MINI INTERN>     1447.18265    946.21240      0.00000      7.12274     32.26577
MINI EXTERN>     6646.27338     -0.83182      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        64
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2133 ATOM PAIRS WERE FOUND FOR ATOM LIST
      221 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2116 ATOM PAIRS WERE FOUND FOR ATOM LIST
      208 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   8663.95696    414.26816     65.37016      0.01537
MINI INTERN>     1265.59188    816.07627      0.00000      6.35024     45.83205
MINI EXTERN>     6531.70301     -1.59649      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        81
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2121 ATOM PAIRS WERE FOUND FOR ATOM LIST
      205 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        87
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2116 ATOM PAIRS WERE FOUND FOR ATOM LIST
      210 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   8465.60004    198.35692     50.03487      0.01282
MINI INTERN>     1136.56084    720.68936      0.00000      7.33734     56.94848
MINI EXTERN>     6546.39999     -2.33598      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       108
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2109 ATOM PAIRS WERE FOUND FOR ATOM LIST
      214 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       115
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2109 ATOM PAIRS WERE FOUND FOR ATOM LIST
      215 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120   8404.88044     60.71959     67.09987      0.01375
MINI INTERN>     1183.13140    650.94569      0.00000      8.44566     57.61651
MINI EXTERN>     6506.96354     -2.22235      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       139
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2112 ATOM PAIRS WERE FOUND FOR ATOM LIST
      217 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140   8372.16353     32.71692     60.58713      0.01193
MINI INTERN>     1125.39551    643.33130      0.00000      9.85353     58.75544
MINI EXTERN>     6537.05471     -2.22698      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       157
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2113 ATOM PAIRS WERE FOUND FOR ATOM LIST
      224 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160   8358.21499     13.94853     13.52055      0.00403
MINI INTERN>     1131.59048    637.90710      0.00000     11.26165     64.22807
MINI EXTERN>     6515.62813     -2.40044      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   8356.14051      2.07448      9.74867      0.00227
MINI INTERN>     1125.68427    638.84422      0.00000     11.42233     63.81465
MINI EXTERN>     6518.76721     -2.39216      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       191
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2107 ATOM PAIRS WERE FOUND FOR ATOM LIST
      226 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200   8344.16274     11.97777     24.09740      0.00591
MINI INTERN>     1139.78831    619.92085      0.00000     11.55587     57.80321
MINI EXTERN>     6517.11692     -2.02243      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       213
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2098 ATOM PAIRS WERE FOUND FOR ATOM LIST
      233 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220   8321.53601     22.62674     14.76736      0.00554
MINI INTERN>     1120.01783    645.36082      0.00000      9.55017     54.01698
MINI EXTERN>     6493.90641     -1.31620      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       226
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2082 ATOM PAIRS WERE FOUND FOR ATOM LIST
      231 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      240   8295.59227     25.94373     41.91545      0.00866
MINI INTERN>     1093.08994    632.78011      0.00000      7.64857     48.01846
MINI EXTERN>     6515.76416     -1.70898      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       249
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2090 ATOM PAIRS WERE FOUND FOR ATOM LIST
      229 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      260   8276.12814     19.46413     16.74235      0.00488
MINI INTERN>     1088.77580    619.03798      0.00000      8.24380     49.81568
MINI EXTERN>     6512.00893     -1.75405      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280   8269.97686      6.15128      8.04188      0.00274
MINI INTERN>     1098.29312    616.54267      0.00000      8.36263     49.50981
MINI EXTERN>     6498.81703     -1.54840      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       291
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2095 ATOM PAIRS WERE FOUND FOR ATOM LIST
      232 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      300   8266.38040      3.59645      6.17305      0.00154
MINI INTERN>     1092.28887    613.87809      0.00000      8.52594     49.03141
MINI EXTERN>     6504.06120     -1.40511      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      320   8265.05940      1.32100      3.27399      0.00087
MINI INTERN>     1089.43228    613.06869      0.00000      8.63637     49.08199
MINI EXTERN>     6506.12968     -1.28961      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      340   8264.83939      0.22001      3.50134      0.00082
MINI INTERN>     1088.09044    614.11922      0.00000      8.56122     48.93525
MINI EXTERN>     6506.40607     -1.27282      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      360   8264.69842      0.14096      2.26540      0.00046
MINI INTERN>     1087.38500    615.85790      0.00000      8.39294     48.54643
MINI EXTERN>     6505.75276     -1.23661      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      380   8264.66437      0.03405      1.03678      0.00026
MINI INTERN>     1087.68745    616.19533      0.00000      8.36843     48.24140
MINI EXTERN>     6505.36731     -1.19556      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      400   8264.65124      0.01313      0.57202      0.00015
MINI INTERN>     1087.23074    616.04198      0.00000      8.37072     48.13570
MINI EXTERN>     6506.05178     -1.17967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      420   8264.64294      0.00830      0.58957      0.00014
MINI INTERN>     1087.27978    615.95326      0.00000      8.38031     48.09411
MINI EXTERN>     6506.10677     -1.17128      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      440   8264.63929      0.00365      0.33960      0.00008
MINI INTERN>     1087.38755    615.85074      0.00000      8.38366     48.10622
MINI EXTERN>     6506.08294     -1.17182      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      460   8264.63865      0.00064      0.26140      0.00004
MINI INTERN>     1087.09709    615.95128      0.00000      8.38070     48.12128
MINI EXTERN>     6506.26142     -1.17313      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      464   8264.63860      0.00005      0.09412      0.00003
ABNR INTERN>     1087.10824    615.96539      0.00000      8.37972     48.12090
ABNR EXTERN>     6506.23750     -1.17315      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "8264.64"
 Comparing "8264.64" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "8264.64"
 Comparing "8264.64" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "8264.64"
 Comparing "8264.64" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "8264.64"
 Comparing "8264.64" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.797993"
 Parameter: R <- "0.797993"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "8264.64"
Evaluating: 8264.64--9.23186
 Parameter: DELE <- "8273.87"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "8273.87"
Evaluating: 1.00654*8273.87
 Parameter: BETADELE <- "8327.98"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "8327.98"
Evaluating: EXP(-8327.98)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.797993"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.797993".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.797993"
 Comparing "0" and "0.797993".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "10"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "13"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "10"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "10" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.870465"
 Parameter: CHICHOICE1 <- "0.870465"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.870465"
 Parameter: BONDS -> "5"
Evaluating: INT(0.870465*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.900921
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.777019"
 Parameter: CHI <- "0.777019"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.777019"
Evaluating: (0.777019*360)-180.0
 Parameter: CHI4 <- "99.7268"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "99.7268"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3305 ATOM PAIRS WERE FOUND FOR ATOM LIST
      352 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.64847      0.04830
MINI EXTERN>  *************    -26.54270      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3309 ATOM PAIRS WERE FOUND FOR ATOM LIST
      349 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3298 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3304 ATOM PAIRS WERE FOUND FOR ATOM LIST
      391 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3291 ATOM PAIRS WERE FOUND FOR ATOM LIST
      403 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3298 ATOM PAIRS WERE FOUND FOR ATOM LIST
      403 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3288 ATOM PAIRS WERE FOUND FOR ATOM LIST
      413 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  26026.64746*************   1483.03873      0.05547
MINI INTERN>     6952.58765    686.03520      0.00000      8.19630     10.61765
MINI EXTERN>    18373.33152     -4.12085      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3278 ATOM PAIRS WERE FOUND FOR ATOM LIST
      414 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3278 ATOM PAIRS WERE FOUND FOR ATOM LIST
      412 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3277 ATOM PAIRS WERE FOUND FOR ATOM LIST
      414 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        40
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3272 ATOM PAIRS WERE FOUND FOR ATOM LIST
      413 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  15797.66793  10228.97954    676.96894      0.06409
MINI INTERN>     7446.76752    653.14552      0.00000      6.88947     17.26122
MINI EXTERN>     7675.71861     -2.11442      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        44
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3281 ATOM PAIRS WERE FOUND FOR ATOM LIST
      413 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3299 ATOM PAIRS WERE FOUND FOR ATOM LIST
      414 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3283 ATOM PAIRS WERE FOUND FOR ATOM LIST
      420 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3268 ATOM PAIRS WERE FOUND FOR ATOM LIST
      422 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   9522.18685   6275.48108    244.52480      0.03086
MINI INTERN>     4694.99456    600.85295      0.00000      6.09749     14.33937
MINI EXTERN>     4210.09427     -4.19179      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        61
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3281 ATOM PAIRS WERE FOUND FOR ATOM LIST
      421 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        70
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3281 ATOM PAIRS WERE FOUND FOR ATOM LIST
      419 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80   8060.59602   1461.59083    373.00222      0.01486
MINI INTERN>     3657.83530    506.55265      0.00000      6.35108      8.11315
MINI EXTERN>     3883.09779     -1.35394      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        83
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3284 ATOM PAIRS WERE FOUND FOR ATOM LIST
      416 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100   7571.28996    489.30607    147.56873      0.00715
MINI INTERN>     3074.12951    479.97166      0.00000      6.71581      6.46210
MINI EXTERN>     4005.92606     -1.91519      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       109
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3301 ATOM PAIRS WERE FOUND FOR ATOM LIST
      418 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       114
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3318 ATOM PAIRS WERE FOUND FOR ATOM LIST
      417 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       118
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3333 ATOM PAIRS WERE FOUND FOR ATOM LIST
      418 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120   5385.96308   2185.32687    290.34311      0.04761
MINI INTERN>     2191.56483    346.92170      0.00000      8.24083      5.53801
MINI EXTERN>     2837.49088     -3.79316      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       127
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3380 ATOM PAIRS WERE FOUND FOR ATOM LIST
      412 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       133
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3390 ATOM PAIRS WERE FOUND FOR ATOM LIST
      405 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140   4212.91051   1173.05257    237.77802      0.02292
MINI INTERN>     1225.42864    307.86233      0.00000      7.56249      1.50520
MINI EXTERN>     2673.17251     -2.62066      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       145
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3402 ATOM PAIRS WERE FOUND FOR ATOM LIST
      404 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       159
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3411 ATOM PAIRS WERE FOUND FOR ATOM LIST
      391 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160   3691.53069    521.37982     82.60859      0.01104
MINI INTERN>      926.71883    325.23428      0.00000      7.17653      0.46431
MINI EXTERN>     2434.44161     -2.50488      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180   3523.07286    168.45783    152.17025      0.01275
MINI INTERN>      810.13910    310.70061      0.00000      7.39397      0.08837
MINI EXTERN>     2397.33376     -2.58295      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       197
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3412 ATOM PAIRS WERE FOUND FOR ATOM LIST
      386 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200   3367.28428    155.78858     39.52769      0.00614
MINI INTERN>      738.82114    280.80545      0.00000      7.85166      0.23746
MINI EXTERN>     2342.01077     -2.44219      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200   3367.28428    155.78858     39.52769      0.00737
STPD INTERN>      738.82114    280.80545      0.00000      7.85166      0.23746
STPD EXTERN>     2342.01077     -2.44219      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3412 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3412 ATOM PAIRS WERE FOUND FOR ATOM LIST
      386 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   3367.28428    155.78858     39.52769      0.00000
MINI INTERN>      738.82114    280.80545      0.00000      7.85166      0.23746
MINI EXTERN>     2342.01077     -2.44219      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3412 ATOM PAIRS WERE FOUND FOR ATOM LIST
      385 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3455 ATOM PAIRS WERE FOUND FOR ATOM LIST
      381 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   3110.77305    256.51123     59.09378      0.04463
MINI INTERN>      516.10566    342.03672      0.00000      8.75412      5.78447
MINI EXTERN>     2241.08493     -2.99286      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3488 ATOM PAIRS WERE FOUND FOR ATOM LIST
      387 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        27
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3507 ATOM PAIRS WERE FOUND FOR ATOM LIST
      382 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   3081.04729     29.72576     13.82629      0.01634
MINI INTERN>      489.37610    346.38325      0.00000      7.22055      4.71187
MINI EXTERN>     2235.99957     -2.64404      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60   3079.91068      1.13661      2.01839      0.00177
MINI INTERN>      485.12748    346.68002      0.00000      6.93203      4.68707
MINI EXTERN>     2239.07023     -2.58616      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80   3079.89801      0.01267      0.14089      0.00021
MINI INTERN>      484.46804    346.41884      0.00000      6.95416      4.70978
MINI EXTERN>     2239.93949     -2.59230      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>       84   3079.89788      0.00013      0.08848      0.00013
ABNR INTERN>      484.47495    346.44312      0.00000      6.95377      4.71193
ABNR EXTERN>     2239.90653     -2.59242      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "3079.9"
 Comparing "3079.9" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3079.9"
 Comparing "3079.9" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "3079.9"
 Comparing "3079.9" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3079.9"
 Comparing "3079.9" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.350406"
 Parameter: R <- "0.350406"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "3079.9"
Evaluating: 3079.9--9.23186
 Parameter: DELE <- "3089.13"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "3089.13"
Evaluating: 1.00654*3089.13
 Parameter: BETADELE <- "3109.33"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "3109.33"
Evaluating: EXP(-3109.33)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.350406"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.350406".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.350406"
 Comparing "0" and "0.350406".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "11"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "14"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "11"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "11" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.267015"
 Parameter: CHICHOICE1 <- "0.267015"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.267015"
 Parameter: BONDS -> "5"
Evaluating: INT(0.267015*5)
 Parameter: CHICHOICE2 <- "1"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "1"
 Parameter: BONDS -> "5"
 Comparing "1" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "1"
 Parameter: CHICHOICE2 -> "1"
 Comparing "1" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 0.71349
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.62498"
 Parameter: CHI <- "0.62498"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "0.62498"
Evaluating: (0.62498*360)-180.0
 Parameter: CHI1 <- "44.9928"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "44.9928"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI1COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2824 ATOM PAIRS WERE FOUND FOR ATOM LIST
      296 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      8.01521      0.04830
MINI EXTERN>  *************     10.49530      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2824 ATOM PAIRS WERE FOUND FOR ATOM LIST
      299 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2841 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2835 ATOM PAIRS WERE FOUND FOR ATOM LIST
      322 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2807 ATOM PAIRS WERE FOUND FOR ATOM LIST
      325 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2792 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2792 ATOM PAIRS WERE FOUND FOR ATOM LIST
      320 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2811 ATOM PAIRS WERE FOUND FOR ATOM LIST
      329 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2790 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  29604.07895*************   4163.73952      0.13312
MINI INTERN>     6205.60541    577.55072      0.00000      5.71264      2.99090
MINI EXTERN>    22813.85328     -1.63400      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2815 ATOM PAIRS WERE FOUND FOR ATOM LIST
      337 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2807 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2799 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        25
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2801 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        33
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2802 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  19653.81898   9950.25997    615.64397      0.02670
MINI INTERN>     5689.86962    531.85407      0.00000      9.72524      2.22376
MINI EXTERN>    13420.96518     -0.81889      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2803 ATOM PAIRS WERE FOUND FOR ATOM LIST
      316 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2803 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  17070.20728   2583.61171    335.23131      0.01286
MINI INTERN>     4807.98259    432.77945      0.00000      9.10096      2.90685
MINI EXTERN>    11817.86844     -0.43102      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2808 ATOM PAIRS WERE FOUND FOR ATOM LIST
      308 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  14194.53764   2875.66963    486.97782      0.01486
MINI INTERN>     4183.25702    344.90494      0.00000      8.73153      5.42145
MINI EXTERN>     9652.08623      0.13647      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        82
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2798 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        98
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2798 ATOM PAIRS WERE FOUND FOR ATOM LIST
      318 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  12392.84662   1801.69102    757.51967      0.01717
MINI INTERN>     3717.09126    313.25987      0.00000      8.71360      6.07070
MINI EXTERN>     8347.16938      0.54181      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       112
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2796 ATOM PAIRS WERE FOUND FOR ATOM LIST
      322 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  11275.85692   1116.98970    754.66988      0.01984
MINI INTERN>     2990.72903    302.90777      0.00000      8.82637      4.64535
MINI EXTERN>     7967.97793      0.77047      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       125
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2797 ATOM PAIRS WERE FOUND FOR ATOM LIST
      320 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  10724.74007    551.11685    120.15570      0.00398
MINI INTERN>     2768.04592    289.86057      0.00000      8.82733      3.63085
MINI EXTERN>     7653.44951      0.92589      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  10632.22998     92.51009    156.41573      0.00460
MINI INTERN>     2742.88273    281.13006      0.00000      8.59341      3.13730
MINI EXTERN>     7595.48792      0.99857      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  10565.04707     67.18291     57.14922      0.00221
MINI INTERN>     2755.32601    272.86080      0.00000      8.25925      2.79846
MINI EXTERN>     7524.75872      1.04383      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       181
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2795 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200  10528.77824     36.26884     85.51719      0.00256
MINI INTERN>     2754.97297    264.86458      0.00000      7.91328      2.55815
MINI EXTERN>     7497.39353      1.07574      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  10528.77824     36.26884     85.51719      0.00307
STPD INTERN>     2754.97297    264.86458      0.00000      7.91328      2.55815
STPD EXTERN>     7497.39353      1.07574      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2795 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2793 ATOM PAIRS WERE FOUND FOR ATOM LIST
      324 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  10528.77824     36.26884     85.51719      0.00000
MINI INTERN>     2754.97297    264.86458      0.00000      7.91328      2.55815
MINI EXTERN>     7497.39353      1.07574      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2799 ATOM PAIRS WERE FOUND FOR ATOM LIST
      328 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2783 ATOM PAIRS WERE FOUND FOR ATOM LIST
      333 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2787 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2783 ATOM PAIRS WERE FOUND FOR ATOM LIST
      327 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  10244.97427    283.80397     92.25090      0.02288
MINI INTERN>     2775.82897    172.21061      0.00000      6.41827      7.14467
MINI EXTERN>     7282.15836      1.21339      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2793 ATOM PAIRS WERE FOUND FOR ATOM LIST
      319 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2803 ATOM PAIRS WERE FOUND FOR ATOM LIST
      314 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  10094.06353    150.91074     81.22121      0.01272
MINI INTERN>     2693.09999    190.66923      0.00000      6.70328      9.86811
MINI EXTERN>     7192.65391      1.06900      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60  10085.80914      8.25439     25.63462      0.00545
MINI INTERN>     2668.45186    199.65889      0.00000      6.93710      9.19264
MINI EXTERN>     7200.42226      1.14639      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  10081.68697      4.12217      5.45980      0.00184
MINI INTERN>     2672.99987    198.82133      0.00000      7.29079      8.59294
MINI EXTERN>     7192.79520      1.18684      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  10080.12621      1.56076      8.32600      0.00173
MINI INTERN>     2672.88024    192.92078      0.00000      7.70283      7.89811
MINI EXTERN>     7197.50332      1.22094      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  10079.56855      0.55766      2.37379      0.00058
MINI INTERN>     2669.30434    195.34035      0.00000      7.76437      7.71107
MINI EXTERN>     7198.20798      1.24045      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  10079.43480      0.13375      3.08846      0.00055
MINI INTERN>     2671.08018    195.85961      0.00000      7.79307      7.62551
MINI EXTERN>     7195.82544      1.25099      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  10079.40702      0.02778      0.90280      0.00018
MINI INTERN>     2672.11108    195.60278      0.00000      7.79897      7.57672
MINI EXTERN>     7195.06968      1.24779      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  10079.37369      0.03333      0.57491      0.00017
MINI INTERN>     2672.25204    195.24212      0.00000      7.80974      7.44183
MINI EXTERN>     7195.36754      1.26043      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  10079.36434      0.00935      0.70755      0.00016
MINI INTERN>     2672.28785    195.35926      0.00000      7.81762      7.44460
MINI EXTERN>     7195.19070      1.26431      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  10079.36268      0.00165      0.12554      0.00003
MINI INTERN>     2672.23943    195.33711      0.00000      7.82106      7.44384
MINI EXTERN>     7195.25678      1.26447      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      232  10079.36241      0.00027      0.08452      0.00004
ABNR INTERN>     2672.18567    195.31827      0.00000      7.82099      7.44554
ABNR EXTERN>     7195.32775      1.26420      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "10079.4"
 Comparing "10079.4" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "10079.4"
 Comparing "10079.4" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "10079.4"
 Comparing "10079.4" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "10079.4"
 Comparing "10079.4" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "3.531699E-02"
 Parameter: R <- "3.531699E-02"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "10079.4"
Evaluating: 10079.4--9.23186
 Parameter: DELE <- "10088.6"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "10088.6"
Evaluating: 1.00654*10088.6
 Parameter: BETADELE <- "10154.6"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "10154.6"
Evaluating: EXP(-10154.6)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "3.531699E-02"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "3.531699E-02".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "3.531699E-02"
 Comparing "0" and "3.531699E-02".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "12"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "15"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "12"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "12" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.572592"
 Parameter: CHICHOICE1 <- "0.572592"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.572592"
 Parameter: BONDS -> "5"
Evaluating: INT(0.572592*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.559454
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.74498"
 Parameter: CHI <- "0.74498"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.74498"
Evaluating: (0.74498*360)-180.0
 Parameter: CHI2 <- "88.1928"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "88.1928"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3058 ATOM PAIRS WERE FOUND FOR ATOM LIST
      310 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      5.64705      0.04830
MINI EXTERN>  *************     49.20342      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3065 ATOM PAIRS WERE FOUND FOR ATOM LIST
      312 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3051 ATOM PAIRS WERE FOUND FOR ATOM LIST
      323 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3068 ATOM PAIRS WERE FOUND FOR ATOM LIST
      336 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3056 ATOM PAIRS WERE FOUND FOR ATOM LIST
      356 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3049 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3042 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3052 ATOM PAIRS WERE FOUND FOR ATOM LIST
      352 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  21999.77835*************   7213.39174      0.05547
MINI INTERN>     4623.25871    218.14724      0.00000      6.82181      0.34881
MINI EXTERN>    17152.17309     -0.97131      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3050 ATOM PAIRS WERE FOUND FOR ATOM LIST
      365 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  14820.80530   7178.97306   1309.26075      0.02670
MINI INTERN>     4493.78992    172.43805      0.00000      7.90640      0.35640
MINI EXTERN>    10146.34092     -0.02639      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3055 ATOM PAIRS WERE FOUND FOR ATOM LIST
      370 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  12852.97021   1967.83509    700.93872      0.01286
MINI INTERN>     4417.85896    173.41429      0.00000      8.41751      0.14531
MINI EXTERN>     8252.91323      0.22092      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3053 ATOM PAIRS WERE FOUND FOR ATOM LIST
      383 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  12293.75888    559.21133    192.76453      0.00619
MINI INTERN>     4382.53149    194.47406      0.00000      8.66683      0.09235
MINI EXTERN>     7707.73461      0.25955      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  12083.97587    209.78301    402.14708      0.00715
MINI INTERN>     4364.78776    211.75639      0.00000      9.37938      0.27705
MINI EXTERN>     7497.46038      0.31491      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  11899.28317    184.69270    114.39939      0.00344
MINI INTERN>     4379.60666    215.98668      0.00000      9.23740      0.72836
MINI EXTERN>     7293.27741      0.44665      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       130
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3047 ATOM PAIRS WERE FOUND FOR ATOM LIST
      391 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  11827.71989     71.56328    225.79231      0.00398
MINI INTERN>     4395.65335    218.40657      0.00000      9.05295      1.04171
MINI EXTERN>     7203.06278      0.50253      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  11773.13219     54.58770     62.61996      0.00192
MINI INTERN>     4396.39253    219.36633      0.00000      8.92749      1.17508
MINI EXTERN>     7146.78676      0.48400      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  11743.86900     29.26319    121.21819      0.00221
MINI INTERN>     4399.68995    219.42383      0.00000      8.80765      1.23110
MINI EXTERN>     7114.27344      0.44302      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  11717.62771     26.24129     44.72374      0.00107
MINI INTERN>     4408.08245    219.08729      0.00000      8.69113      1.25909
MINI EXTERN>     7080.10525      0.40249      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  11717.62771     26.24129     44.72374      0.00128
STPD INTERN>     4408.08245    219.08729      0.00000      8.69113      1.25909
STPD EXTERN>     7080.10525      0.40249      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3047 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3041 ATOM PAIRS WERE FOUND FOR ATOM LIST
      391 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  11717.62771     26.24129     44.72374      0.00000
MINI INTERN>     4408.08245    219.08729      0.00000      8.69113      1.25909
MINI EXTERN>     7080.10525      0.40249      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3028 ATOM PAIRS WERE FOUND FOR ATOM LIST
      388 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3049 ATOM PAIRS WERE FOUND FOR ATOM LIST
      382 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  11542.27596    175.35175     37.35819      0.00807
MINI INTERN>     4420.91228    246.32476      0.00000      7.31014      1.82600
MINI EXTERN>     6865.68650      0.21628      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40  11533.37270      8.90326     59.99993      0.00796
MINI INTERN>     4418.44763    241.47139      0.00000      7.61728      1.72854
MINI EXTERN>     6863.84899      0.25887      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60  11525.99449      7.37821     13.60888      0.00568
MINI INTERN>     4405.32977    250.42426      0.00000      7.45763      1.50528
MINI EXTERN>     6860.99839      0.27916      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  11524.92378      1.07071      5.72727      0.00135
MINI INTERN>     4404.52755    246.20970      0.00000      7.21315      1.54610
MINI EXTERN>     6865.13030      0.29699      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       100
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3068 ATOM PAIRS WERE FOUND FOR ATOM LIST
      386 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  11524.83304      0.09074      1.90136      0.00046
MINI INTERN>     4404.03344    246.45518      0.00000      7.10185      1.52740
MINI EXTERN>     6865.41466      0.30050      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  11524.82355      0.00949      0.90174      0.00015
MINI INTERN>     4404.26750    246.81407      0.00000      7.06420      1.51828
MINI EXTERN>     6864.86016      0.29932      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  11524.82253      0.00102      1.01472      0.00009
MINI INTERN>     4404.35198    246.73838      0.00000      7.06485      1.52377
MINI EXTERN>     6864.84500      0.29854      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      152  11524.82206      0.00047      0.04396      0.00004
ABNR INTERN>     4404.28032    246.66998      0.00000      7.06776      1.52761
ABNR EXTERN>     6864.97848      0.29791      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11524.8"
 Comparing "11524.8" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "11524.8"
 Comparing "11524.8" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "11524.8"
 Comparing "11524.8" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "11524.8"
 Comparing "11524.8" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.886574"
 Parameter: R <- "0.886574"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "11524.8"
Evaluating: 11524.8--9.23186
 Parameter: DELE <- "11534"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "11534"
Evaluating: 1.00654*11534
 Parameter: BETADELE <- "11609.4"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "11609.4"
Evaluating: EXP(-11609.4)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.886574"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.886574".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.886574"
 Comparing "0" and "0.886574".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "13"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "16"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "13"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "13" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.651285"
 Parameter: CHICHOICE1 <- "0.651285"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.651285"
 Parameter: BONDS -> "5"
Evaluating: INT(0.651285*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.151925
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.408984"
 Parameter: CHI <- "0.408984"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.408984"
Evaluating: (0.408984*360)-180.0
 Parameter: CHI3 <- "-32.7658"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "-32.7658"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1777 ATOM PAIRS WERE FOUND FOR ATOM LIST
      204 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  37521.50824 -25996.68618  35075.53767      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      7.24406      0.04830
MINI EXTERN>    37490.84011      1.37873      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1773 ATOM PAIRS WERE FOUND FOR ATOM LIST
      194 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1754 ATOM PAIRS WERE FOUND FOR ATOM LIST
      185 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1729 ATOM PAIRS WERE FOUND FOR ATOM LIST
      186 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    144.08131  37377.42694     16.48079      0.02311
MINI INTERN>       18.49685     51.53527      0.00000      8.14744      0.51091
MINI EXTERN>       64.66748      0.72336      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1713 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     50.77830     93.30301     13.31957      0.01113
MINI INTERN>        5.02315     15.25378      0.00000      4.06641      0.18387
MINI EXTERN>       25.74136      0.50973      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1683 ATOM PAIRS WERE FOUND FOR ATOM LIST
      189 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     31.87169     18.90661     16.78171      0.01286
MINI INTERN>        3.70515     10.24196      0.00000      3.53619      0.10497
MINI EXTERN>       13.80612      0.47730      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     20.34159     11.53011      7.90085      0.00619
MINI INTERN>        1.39882      7.49845      0.00000      3.47065      0.12273
MINI EXTERN>        7.28196      0.56898      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        93
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1625 ATOM PAIRS WERE FOUND FOR ATOM LIST
      189 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     15.06378      5.27780      9.21755      0.00715
MINI INTERN>        1.28986      5.98010      0.00000      3.44949      0.15658
MINI EXTERN>        3.55068      0.63708      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     10.70214      4.36164      2.69293      0.00344
MINI INTERN>        0.54378      4.84807      0.00000      3.41946      0.18721
MINI EXTERN>        1.04449      0.65914      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      8.22816      2.47399      5.66549      0.00398
MINI INTERN>        0.64850      4.17431      0.00000      3.37281      0.19884
MINI EXTERN>       -0.81027      0.64397      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160      6.33026      1.89790      6.02873      0.00460
MINI INTERN>        0.63135      3.71300      0.00000      3.33027      0.20035
MINI EXTERN>       -2.14662      0.60191      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180      4.53479      1.79546      2.80104      0.00221
MINI INTERN>        0.35284      3.37050      0.00000      3.28463      0.18873
MINI EXTERN>       -3.21178      0.54988      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       195
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1571 ATOM PAIRS WERE FOUND FOR ATOM LIST
      192 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200      3.32865      1.20614      3.34098      0.00256
MINI INTERN>        0.34805      3.10689      0.00000      3.25732      0.18838
MINI EXTERN>       -4.06515      0.49316      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      3.32865      1.20614      3.34098      0.00307
STPD INTERN>        0.34805      3.10689      0.00000      3.25732      0.18838
STPD EXTERN>       -4.06515      0.49316      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1571 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1567 ATOM PAIRS WERE FOUND FOR ATOM LIST
      190 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      3.32865      1.20614      3.34098      0.00000
MINI INTERN>        0.34805      3.10689      0.00000      3.25732      0.18838
MINI EXTERN>       -4.06515      0.49316      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1514 ATOM PAIRS WERE FOUND FOR ATOM LIST
      187 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1448 ATOM PAIRS WERE FOUND FOR ATOM LIST
      176 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -3.99973      7.32838      1.21735      0.00667
MINI INTERN>        0.20481      2.07502      0.00000      3.33635      0.29966
MINI EXTERN>       -9.59327     -0.32231      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     -4.59421      0.59448      0.77125      0.00375
MINI INTERN>        0.19366      1.91094      0.00000      3.42743      0.29610
MINI EXTERN>      -10.09074     -0.33160      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1458 ATOM PAIRS WERE FOUND FOR ATOM LIST
      177 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -4.82045      0.22623      1.35204      0.00587
MINI INTERN>        0.18689      1.83174      0.00000      3.37037      0.28097
MINI EXTERN>      -10.09361     -0.39681      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -5.00282      0.18237      0.67158      0.00330
MINI INTERN>        0.14325      1.93442      0.00000      3.28348      0.28904
MINI EXTERN>      -10.20497     -0.44803      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -5.12886      0.12604      0.23293      0.00186
MINI INTERN>        0.14836      1.90419      0.00000      3.30590      0.27823
MINI EXTERN>      -10.27147     -0.49409      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       109
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1474 ATOM PAIRS WERE FOUND FOR ATOM LIST
      178 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -5.46488      0.33601      0.56445      0.00291
MINI INTERN>        0.16558      1.86802      0.00000      3.32600      0.29877
MINI EXTERN>      -10.49162     -0.63162      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -5.70615      0.24127      0.50580      0.00273
MINI INTERN>        0.15194      1.85619      0.00000      3.29695      0.29715
MINI EXTERN>      -10.71070     -0.59768      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       160
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1502 ATOM PAIRS WERE FOUND FOR ATOM LIST
      179 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -5.80720      0.10105      0.35841      0.00256
MINI INTERN>        0.14805      1.89443      0.00000      3.27480      0.31824
MINI EXTERN>      -10.90103     -0.54168      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       179
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1580 ATOM PAIRS WERE FOUND FOR ATOM LIST
      185 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     -6.16543      0.35823      1.17390      0.00667
MINI INTERN>        0.26517      2.14086      0.00000      3.33050      0.39585
MINI EXTERN>      -11.76505     -0.53277      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       185
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1688 ATOM PAIRS WERE FOUND FOR ATOM LIST
      194 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       196
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1770 ATOM PAIRS WERE FOUND FOR ATOM LIST
      200 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     -7.63340      1.46797      3.95361      0.01931
MINI INTERN>        0.31667      2.20586      0.00000      3.51138      0.47015
MINI EXTERN>      -13.48701     -0.65046      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       201
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1856 ATOM PAIRS WERE FOUND FOR ATOM LIST
      216 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       211
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1939 ATOM PAIRS WERE FOUND FOR ATOM LIST
      225 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220     -9.14175      1.50835      1.21523      0.00644
MINI INTERN>        0.13817      2.14809      0.00000      3.48027      0.40374
MINI EXTERN>      -14.32952     -0.98251      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -9.68781      0.54606      0.69153      0.00362
MINI INTERN>        0.12724      2.13366      0.00000      3.52009      0.54558
MINI EXTERN>      -14.87272     -1.14167      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -9.82785      0.14004      0.74700      0.00340
MINI INTERN>        0.12952      2.08742      0.00000      3.49391      0.57451
MINI EXTERN>      -14.88350     -1.22970      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -9.89088      0.06303      0.34799      0.00191
MINI INTERN>        0.13036      2.10672      0.00000      3.51337      0.55654
MINI EXTERN>      -14.94396     -1.25391      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       298
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1954 ATOM PAIRS WERE FOUND FOR ATOM LIST
      222 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      300     -9.98756      0.09668      0.30283      0.00180
MINI INTERN>        0.12371      2.07524      0.00000      3.43749      0.56624
MINI EXTERN>      -14.93520     -1.25503      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      320    -10.08826      0.10070      0.63332      0.00281
MINI INTERN>        0.12395      1.98030      0.00000      3.37739      0.49588
MINI EXTERN>      -14.84374     -1.22204      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      340    -10.14984      0.06158      0.48670      0.00263
MINI INTERN>        0.12770      2.00493      0.00000      3.37759      0.51452
MINI EXTERN>      -14.92253     -1.25205      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      359    -10.16795      0.01811      0.08188      0.00089
ABNR INTERN>        0.12688      2.01697      0.00000      3.38599      0.51036
ABNR EXTERN>      -14.94199     -1.26617      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-10.1679"
 Comparing "-10.1679" and "-9.23186".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "-10.1679"
 Comparing "-10.1679" and "-9.23186".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1120.1071  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.944700
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.9447"
 Parameter: RMSD <- "8.9447"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.9447"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.9447" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.9447"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.9447" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.9447"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.9447" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "4"
 Comparing "2" and "4".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    810.6819  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    7.609589
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "7.60959"
 Parameter: RMSD <- "7.60959"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "7.60959"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60959" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "7.60959"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60959" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "7.60959"
 Parameter: RMSTOL -> "0.05"
 Comparing "7.60959" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "4"
 Comparing "3" and "4".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    119.5100  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    2.921717
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "2.92172"
 Parameter: RMSD <- "2.92172"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "2.92172"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.92172" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "2.92172"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.92172" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "2.92172"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.92172" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "4"
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS     45.2454  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    1.797725
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "1.79772"
 Parameter: RMSD <- "1.79772"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "1.79772"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.79772" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "1.79772"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.79772" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "1.79772"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.79772" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "4"
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.23186"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-10.1679"
 Comparing "-10.1679" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.23186"
 RDCMND substituted energy or value "?ENER" to "-10.1679"
 Comparing "-10.1679" and "-9.23186".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "1.79772"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1.79772" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "1.79772"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.79772" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "5"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "5"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "5"
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "5"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "5" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "5"
 Comparing "5" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "5"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame5.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -10.1679 0.126882 2.01697 3.38599 -14.942 -1.26617
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-10.1679"
 Parameter: ELAST <- "-10.1679"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "17"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "13"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "13" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.797658"
 Parameter: CHICHOICE1 <- "0.797658"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.797658"
 Parameter: BONDS -> "5"
Evaluating: INT(0.797658*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.233421
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "9.90195E-02"
 Parameter: CHI <- "9.90195E-02"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "9.90195E-02"
Evaluating: (9.90195E-02*360)-180.0
 Parameter: CHI3 <- "-144.353"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "-144.353"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3148 ATOM PAIRS WERE FOUND FOR ATOM LIST
      313 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      6.87014      0.04830
MINI EXTERN>  *************     -0.03295      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3142 ATOM PAIRS WERE FOUND FOR ATOM LIST
      320 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3150 ATOM PAIRS WERE FOUND FOR ATOM LIST
      330 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3147 ATOM PAIRS WERE FOUND FOR ATOM LIST
      337 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3142 ATOM PAIRS WERE FOUND FOR ATOM LIST
      348 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3126 ATOM PAIRS WERE FOUND FOR ATOM LIST
      343 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3124 ATOM PAIRS WERE FOUND FOR ATOM LIST
      353 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3124 ATOM PAIRS WERE FOUND FOR ATOM LIST
      355 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  18702.85959*************   2298.54216      0.05547
MINI INTERN>     4554.68642    321.38490      0.00000      7.35484      0.72928
MINI EXTERN>    13819.40687     -0.70271      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3155 ATOM PAIRS WERE FOUND FOR ATOM LIST
      371 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  14062.06525   4640.79433    537.23936      0.01113
MINI INTERN>     4800.28422    321.31536      0.00000      7.79191      0.13234
MINI EXTERN>     8932.15359      0.38784      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3176 ATOM PAIRS WERE FOUND FOR ATOM LIST
      384 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  13303.09081    758.97444    736.28147      0.01286
MINI INTERN>     4692.81669    363.67152      0.00000      8.72952      0.27042
MINI EXTERN>     8236.97281      0.62984      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  12873.38923    429.70158    385.87434      0.00619
MINI INTERN>     4705.30664    382.39539      0.00000      9.27895      1.07804
MINI EXTERN>     7774.65189      0.67833      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  12704.67499    168.71424    163.65187      0.00298
MINI INTERN>     4705.66651    386.57305      0.00000      9.34233      1.66093
MINI EXTERN>     7600.80755      0.62462      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  12628.05210     76.62289    192.43792      0.00344
MINI INTERN>     4716.55190    385.18132      0.00000      9.33306      1.98561
MINI EXTERN>     7514.45408      0.54613      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       125
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3159 ATOM PAIRS WERE FOUND FOR ATOM LIST
      387 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  12570.42532     57.62678     48.45783      0.00166
MINI INTERN>     4728.94312    381.68790      0.00000      9.29112      2.17409
MINI EXTERN>     7447.84354      0.48554      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160  12530.91101     39.51431     70.73179      0.00192
MINI INTERN>     4732.59461    377.09941      0.00000      9.22353      2.30987
MINI EXTERN>     7409.24231      0.44128      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  12503.71358     27.19743    123.97779      0.00221
MINI INTERN>     4735.02638    372.54384      0.00000      9.14905      2.40220
MINI EXTERN>     7384.17781      0.41430      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  12480.33699     23.37659    145.17245      0.00256
MINI INTERN>     4735.92611    368.10995      0.00000      9.06883      2.47606
MINI EXTERN>     7364.35958      0.39645      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  12480.33699     23.37659    145.17245      0.00128
STPD INTERN>     4735.92611    368.10995      0.00000      9.06883      2.47606
STPD EXTERN>     7364.35958      0.39645      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     3159 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3152 ATOM PAIRS WERE FOUND FOR ATOM LIST
      387 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  12479.77922      0.55777    116.26385      0.00000
MINI INTERN>     4726.48175    368.34356      0.00000      9.07235      2.47321
MINI EXTERN>     7373.01129      0.39706      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3157 ATOM PAIRS WERE FOUND FOR ATOM LIST
      394 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  12352.73247    127.04675    100.77716      0.01741
MINI INTERN>     4750.34940    352.84946      0.00000      8.29280      2.89780
MINI EXTERN>     7237.76348      0.57952      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3173 ATOM PAIRS WERE FOUND FOR ATOM LIST
      398 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  12323.79415     28.93832     75.03333      0.01326
MINI INTERN>     4744.19851    355.55745      0.00000      8.46491      2.61288
MINI EXTERN>     7212.34579      0.61462      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     3172 ATOM PAIRS WERE FOUND FOR ATOM LIST
      402 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  12312.46553     11.32863     29.02142      0.00332
MINI INTERN>     4723.35045    344.95271      0.00000      7.83752      2.77612
MINI EXTERN>     7232.90749      0.64124      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80  12311.44957      1.01595      1.24941      0.00100
MINI INTERN>     4727.30107    343.16729      0.00000      7.71656      2.72970
MINI EXTERN>     7229.89790      0.63706      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  12311.39014      0.05943      2.23447      0.00034
MINI INTERN>     4729.10064    342.19745      0.00000      7.72303      2.71940
MINI EXTERN>     7229.01714      0.63248      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  12311.38488      0.00527      0.36165      0.00011
MINI INTERN>     4728.88428    342.03661      0.00000      7.73327      2.71895
MINI EXTERN>     7229.38079      0.63097      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      122  12311.38470      0.00017      0.09051      0.00008
ABNR INTERN>     4728.92506    342.00443      0.00000      7.73525      2.72086
ABNR EXTERN>     7229.36812      0.63098      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-10.1679"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "12311.4"
 Comparing "12311.4" and "-10.1679".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "12311.4"
 Comparing "12311.4" and "-10.1679".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-10.1679"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "12311.4"
 Comparing "12311.4" and "-10.1679".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "12311.4"
 Comparing "12311.4" and "-10.1679".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.220838"
 Parameter: R <- "0.220838"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "12311.4"
Evaluating: 12311.4--10.1679
 Parameter: DELE <- "12321.6"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "12321.6"
Evaluating: 1.00654*12321.6
 Parameter: BETADELE <- "12402.2"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "12402.2"
Evaluating: EXP(-12402.2)
 Parameter: DELN <- "0"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0"
 Parameter: R -> "0.220838"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0" and "0.220838".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0"
 Parameter: R -> "0.220838"
 Comparing "0" and "0.220838".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "14"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "18"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "14"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "14" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.630436"
 Parameter: CHICHOICE1 <- "0.630436"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.630436"
 Parameter: BONDS -> "5"
Evaluating: INT(0.630436*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.738294
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.513068"
 Parameter: CHI <- "0.513068"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.513068"
Evaluating: (0.513068*360)-180.0
 Parameter: CHI3 <- "4.70448"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "4.70448"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1606 ATOM PAIRS WERE FOUND FOR ATOM LIST
      203 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0    126.94266  12184.44204     74.00695      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      9.53348      0.04830
MINI EXTERN>       95.27542      0.08841      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1576 ATOM PAIRS WERE FOUND FOR ATOM LIST
      197 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     22.05700    104.88566     10.98475      0.00963
MINI INTERN>        1.84971      6.53836      0.00000      7.56540      0.46824
MINI EXTERN>        5.89115     -0.25587      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     13.56376      8.49324      5.71968      0.00464
MINI INTERN>        0.65747      4.86959      0.00000      7.13995      0.50290
MINI EXTERN>        0.61116     -0.21731      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      9.40282      4.16094      7.03829      0.00536
MINI INTERN>        0.64183      4.24327      0.00000      6.67414      0.44336
MINI EXTERN>       -2.46165     -0.13812      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80      6.21954      3.18328      1.73342      0.00258
MINI INTERN>        0.26861      3.73734      0.00000      6.22555      0.41824
MINI EXTERN>       -4.35232     -0.07788      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100      4.11912      2.10042      3.87875      0.00298
MINI INTERN>        0.31121      3.52663      0.00000      5.73413      0.40871
MINI EXTERN>       -5.83869     -0.02286      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      2.37868      1.74045      4.43268      0.00344
MINI INTERN>        0.30724      3.27261      0.00000      5.24454      0.40787
MINI EXTERN>       -6.87767      0.02408      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       121
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1508 ATOM PAIRS WERE FOUND FOR ATOM LIST
      193 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140      0.86919      1.50949      5.07483      0.00398
MINI INTERN>        0.32287      2.88994      0.00000      4.75881      0.41384
MINI EXTERN>       -7.57504      0.05877      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -0.44641      1.31560      1.43208      0.00192
MINI INTERN>        0.12560      2.58558      0.00000      4.37697      0.39803
MINI EXTERN>       -8.00660      0.07402      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -1.12308      0.67667      0.80944      0.00092
MINI INTERN>        0.10499      2.45487      0.00000      4.13250      0.40585
MINI EXTERN>       -8.31268      0.09140      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -1.56637      0.44329      0.67591      0.00107
MINI INTERN>        0.10149      2.41397      0.00000      3.98512      0.40951
MINI EXTERN>       -8.58005      0.10360      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -1.56637      0.44329      0.67591      0.00128
STPD INTERN>        0.10149      2.41397      0.00000      3.98512      0.40951
STPD EXTERN>       -8.58005      0.10360      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1508 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1484 ATOM PAIRS WERE FOUND FOR ATOM LIST
      190 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -1.56637      0.44329      0.67591      0.00000
MINI INTERN>        0.10149      2.41397      0.00000      3.98512      0.40951
MINI EXTERN>       -8.58005      0.10360      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20     -3.43484      1.86847      0.50440      0.00320
MINI INTERN>        0.15165      3.18310      0.00000      3.03666      0.51074
MINI EXTERN>      -10.59616      0.27916      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1408 ATOM PAIRS WERE FOUND FOR ATOM LIST
      189 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -3.94333      0.50850      0.89473      0.00501
MINI INTERN>        0.16326      2.82142      0.00000      2.37350      0.52885
MINI EXTERN>      -10.33643      0.50606      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -4.18219      0.23886      0.35230      0.00282
MINI INTERN>        0.12743      2.29474      0.00000      2.41289      0.42089
MINI EXTERN>       -9.98142      0.54327      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -4.28231      0.10012      0.46864      0.00264
MINI INTERN>        0.13312      2.26477      0.00000      2.32239      0.49993
MINI EXTERN>       -9.99849      0.49597      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -4.37572      0.09341      0.90095      0.00413
MINI INTERN>        0.14525      2.42657      0.00000      2.33066      0.49034
MINI EXTERN>      -10.19737      0.42883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       105
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1414 ATOM PAIRS WERE FOUND FOR ATOM LIST
      193 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -4.73683      0.36111      0.35616      0.00233
MINI INTERN>        0.18164      2.64959      0.00000      2.07923      0.53314
MINI EXTERN>      -10.42148      0.24104      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -4.98720      0.25036      0.57904      0.00364
MINI INTERN>        0.15966      2.58577      0.00000      1.86087      0.55610
MINI EXTERN>      -10.37935      0.22975      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -5.21064      0.22344      0.36216      0.00205
MINI INTERN>        0.15480      2.18706      0.00000      1.73309      0.43549
MINI EXTERN>      -10.07458      0.35350      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -5.34994      0.13930      0.52576      0.00320
MINI INTERN>        0.15217      2.16937      0.00000      1.77595      0.49044
MINI EXTERN>      -10.24592      0.30805      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       187
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1439 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       192
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1473 ATOM PAIRS WERE FOUND FOR ATOM LIST
      203 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       196
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1497 ATOM PAIRS WERE FOUND FOR ATOM LIST
      207 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     -6.37941      1.02947      2.67015      0.01373
MINI INTERN>        0.13617      2.55187      0.00000      1.54005      0.88217
MINI EXTERN>      -11.00511     -0.48456      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       218
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1529 ATOM PAIRS WERE FOUND FOR ATOM LIST
      208 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220     -7.58483      1.20542      0.84555      0.00515
MINI INTERN>        0.15383      2.25483      0.00000      1.23771      0.55090
MINI EXTERN>      -11.26057     -0.52153      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -8.01527      0.43044      0.59784      0.00290
MINI INTERN>        0.13530      1.92073      0.00000      0.88072      0.37577
MINI EXTERN>      -10.94602     -0.38177      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -8.17580      0.16053      0.41698      0.00272
MINI INTERN>        0.12019      1.95049      0.00000      0.73956      0.50957
MINI EXTERN>      -11.14156     -0.35406      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -8.23931      0.06351      0.16123      0.00153
MINI INTERN>        0.13547      1.85407      0.00000      0.75633      0.39197
MINI EXTERN>      -11.06691     -0.31025      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300     -8.34148      0.10216      0.39206      0.00239
MINI INTERN>        0.15073      1.89633      0.00000      0.60425      0.42763
MINI EXTERN>      -11.19976     -0.22066      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       304
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1515 ATOM PAIRS WERE FOUND FOR ATOM LIST
      212 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       308
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1507 ATOM PAIRS WERE FOUND FOR ATOM LIST
      210 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       309
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1514 ATOM PAIRS WERE FOUND FOR ATOM LIST
      210 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       319
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1515 ATOM PAIRS WERE FOUND FOR ATOM LIST
      210 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      320     -8.65211      0.31063      0.80125      0.00554
MINI INTERN>        0.16903      1.88868      0.00000      0.37306      0.38228
MINI EXTERN>      -11.41202     -0.05314      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       323
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1521 ATOM PAIRS WERE FOUND FOR ATOM LIST
      209 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      340     -8.95965      0.30754      1.62978      0.00676
MINI INTERN>        0.13549      1.91932      0.00000      0.21295      0.40060
MINI EXTERN>      -11.44694     -0.18106      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      360     -9.10862      0.14897      0.41926      0.00228
MINI INTERN>        0.14973      1.92042      0.00000      0.21542      0.38098
MINI EXTERN>      -11.56322     -0.21196      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      380     -9.22875      0.12013      0.45914      0.00214
MINI INTERN>        0.12919      1.88302      0.00000      0.23096      0.41396
MINI EXTERN>      -11.60150     -0.28438      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       384
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1559 ATOM PAIRS WERE FOUND FOR ATOM LIST
      209 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      400     -9.27742      0.04867      0.18871      0.00121
MINI INTERN>        0.12724      1.81109      0.00000      0.22855      0.41698
MINI EXTERN>      -11.56962     -0.29167      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      420     -9.36897      0.09155      0.33556      0.00189
MINI INTERN>        0.14199      1.82420      0.00000      0.22111      0.39595
MINI EXTERN>      -11.62253     -0.32971      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      440     -9.47319      0.10421      0.17269      0.00106
MINI INTERN>        0.13997      1.84779      0.00000      0.24713      0.39102
MINI EXTERN>      -11.70467     -0.39442      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      460     -9.51853      0.04534      0.10251      0.00060
MINI INTERN>        0.13070      1.83191      0.00000      0.28717      0.39656
MINI EXTERN>      -11.73345     -0.43141      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       475
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1564 ATOM PAIRS WERE FOUND FOR ATOM LIST
      211 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      480     -9.57665      0.05812      0.28283      0.00156
MINI INTERN>        0.13180      1.83473      0.00000      0.24264      0.41764
MINI EXTERN>      -11.77784     -0.42561      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      500     -9.60566      0.02901      0.19833      0.00146
MINI INTERN>        0.12965      1.82666      0.00000      0.24490      0.38463
MINI EXTERN>      -11.76208     -0.42941      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      520     -9.66149      0.05584      0.14599      0.00082
MINI INTERN>        0.12282      1.84218      0.00000      0.25184      0.39052
MINI EXTERN>      -11.79750     -0.47135      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      529     -9.66664      0.00514      0.09991      0.00080
ABNR INTERN>        0.12591      1.82421      0.00000      0.24934      0.39948
ABNR EXTERN>      -11.79684     -0.46873      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-10.1679"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-9.66664"
 Comparing "-9.66664" and "-10.1679".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "-9.66664"
 Comparing "-9.66664" and "-10.1679".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-10.1679"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-9.66664"
 Comparing "-9.66664" and "-10.1679".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "-9.66664"
 Comparing "-9.66664" and "-10.1679".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.128571"
 Parameter: R <- "0.128571"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-10.1679"
 RDCMND substituted energy or value "?ENER" to "-9.66664"
Evaluating: -9.66664--10.1679
 Parameter: DELE <- "0.50126"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "0.50126"
Evaluating: 1.00654*0.50126
 Parameter: BETADELE <- "0.504538"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "0.504538"
Evaluating: EXP(-0.504538)
 Parameter: DELN <- "0.603784"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.603784"
 Parameter: R -> "0.128571"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.603784" and "0.128571".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.603784"
 Parameter: R -> "0.128571"
 Comparing "0.603784" and "0.128571".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.603784"
 Parameter: R -> "0.128571"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.603784" and "0.128571".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.603784"
 Parameter: R -> "0.128571"
 Comparing "0.603784" and "0.128571".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    463.3196  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    5.752761
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "5.75276"
 Parameter: RMSD <- "5.75276"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "5.75276"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.75276" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "5.75276"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.75276" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "5.75276"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.75276" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "5"
 Comparing "2" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    147.8136  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.249325
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.24932"
 Parameter: RMSD <- "3.24932"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.24932"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.24932" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.24932"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.24932" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.24932"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.24932" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "5"
 Comparing "3" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    395.7095  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    5.316480
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "5.31648"
 Parameter: RMSD <- "5.31648"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "5.31648"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.31648" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "5.31648"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.31648" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "5.31648"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.31648" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "5"
 Comparing "4" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    320.5369  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    4.784924
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "4.78492"
 Parameter: RMSD <- "4.78492"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "4.78492"
 Parameter: RMSTOL -> "0.05"
 Comparing "4.78492" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "4.78492"
 Parameter: RMSTOL -> "0.05"
 Comparing "4.78492" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "4.78492"
 Parameter: RMSTOL -> "0.05"
 Comparing "4.78492" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "5"
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    366.0940  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    5.113665
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "5.11367"
 Parameter: RMSD <- "5.11367"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "5.11367"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.11367" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "5.11367"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.11367" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "5.11367"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.11367" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "5"
 Comparing "6" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "5.11367"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "5.11367" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "5.11367"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.11367" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "6"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "6"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "6"
 Comparing "6" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "6"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "6"
 Comparing "6" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "6"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame6.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -9.66664 0.125907 1.82421 0.249341 -11.7968 -0.468726
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-9.66664"
 Parameter: ELAST <- "-9.66664"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "19"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "14"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "14" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.897751"
 Parameter: CHICHOICE1 <- "0.897751"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.897751"
 Parameter: BONDS -> "5"
Evaluating: INT(0.897751*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.505435
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.850145"
 Parameter: CHI <- "0.850145"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.850145"
Evaluating: (0.850145*360)-180.0
 Parameter: CHI4 <- "126.052"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "126.052"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1709 ATOM PAIRS WERE FOUND FOR ATOM LIST
      222 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     71.93575    -81.60238     46.78995      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.29623      0.04830
MINI EXTERN>       38.88799      0.70618      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20     16.45921     55.47653     12.43722      0.00963
MINI INTERN>        2.38234      4.07686      0.00000      7.74643      0.30552
MINI EXTERN>        1.77445      0.17361      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1679 ATOM PAIRS WERE FOUND FOR ATOM LIST
      215 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     10.25788      6.20134      5.85460      0.00464
MINI INTERN>        1.08717      3.47333      0.00000      7.01742      0.36587
MINI EXTERN>       -1.83737      0.15146      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      7.30246      2.95542      6.90837      0.00536
MINI INTERN>        0.94104      3.22424      0.00000      6.51778      0.42945
MINI EXTERN>       -3.97691      0.16687      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80      4.82796      2.47449      2.02712      0.00258
MINI INTERN>        0.43284      3.06479      0.00000      6.10423      0.46888
MINI EXTERN>       -5.43510      0.19233      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100      3.44125      1.38672      4.28143      0.00298
MINI INTERN>        0.45187      3.01060      0.00000      5.75434      0.50102
MINI EXTERN>       -6.49645      0.21986      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      2.24339      1.19785      1.29408      0.00144
MINI INTERN>        0.26633      2.95256      0.00000      5.48111      0.53276
MINI EXTERN>       -7.23375      0.24439      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      1.42040      0.82299      1.26550      0.00166
MINI INTERN>        0.22565      2.95139      0.00000      5.24354      0.55034
MINI EXTERN>       -7.81317      0.26265      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160      0.80114      0.61926      2.66421      0.00192
MINI INTERN>        0.23826      2.96519      0.00000      5.03465      0.56688
MINI EXTERN>       -8.28125      0.27742      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180      0.31111      0.49002      2.84282      0.00221
MINI INTERN>        0.22632      2.98404      0.00000      4.86824      0.57499
MINI EXTERN>       -8.62974      0.28726      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -0.17042      0.48153      0.68704      0.00107
MINI INTERN>        0.16211      3.00595      0.00000      4.72160      0.57026
MINI EXTERN>       -8.92345      0.29311      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -0.17042      0.48153      0.68704      0.00128
STPD INTERN>        0.16211      3.00595      0.00000      4.72160      0.57026
STPD EXTERN>       -8.92345      0.29311      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1679 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1593 ATOM PAIRS WERE FOUND FOR ATOM LIST
      210 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -0.17042      0.48153      0.68704      0.00000
MINI INTERN>        0.16211      3.00595      0.00000      4.72160      0.57026
MINI EXTERN>       -8.92345      0.29311      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1518 ATOM PAIRS WERE FOUND FOR ATOM LIST
      205 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -4.29637      4.12595      2.77639      0.01830
MINI INTERN>        0.14701      2.62121      0.00000      1.91397      0.35284
MINI EXTERN>       -9.77003      0.43863      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1484 ATOM PAIRS WERE FOUND FOR ATOM LIST
      203 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -4.91214      0.61577      0.93766      0.00494
MINI INTERN>        0.12536      2.17826      0.00000      2.25726      0.39404
MINI EXTERN>      -10.10952      0.24245      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -5.03600      0.12386      0.55331      0.00278
MINI INTERN>        0.12448      2.28628      0.00000      2.19675      0.47078
MINI EXTERN>      -10.33565      0.22136      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -5.55575      0.51975      1.05968      0.00725
MINI INTERN>        0.21768      2.19498      0.00000      1.66509      0.59417
MINI EXTERN>      -10.41430      0.18663      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        81
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1489 ATOM PAIRS WERE FOUND FOR ATOM LIST
      206 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -6.25341      0.69767      0.84291      0.00454
MINI INTERN>        0.13926      2.04275      0.00000      1.26466      0.45333
MINI EXTERN>      -10.35721      0.20379      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -6.54249      0.28907      0.77334      0.00425
MINI INTERN>        0.16703      1.80815      0.00000      1.12795      0.36486
MINI EXTERN>      -10.24361      0.23312      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       123
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1505 ATOM PAIRS WERE FOUND FOR ATOM LIST
      207 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     -6.69664      0.15415      0.37442      0.00239
MINI INTERN>        0.13020      1.91948      0.00000      1.09915      0.40350
MINI EXTERN>      -10.47991      0.23095      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -6.79197      0.09533      0.22272      0.00135
MINI INTERN>        0.13362      1.98696      0.00000      1.03661      0.43050
MINI EXTERN>      -10.59004      0.21038      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       174
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1534 ATOM PAIRS WERE FOUND FOR ATOM LIST
      214 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     -7.03792      0.24595      1.15085      0.00650
MINI INTERN>        0.22025      2.62655      0.00000      0.96502      0.67074
MINI EXTERN>      -11.56994      0.04946      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       182
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1575 ATOM PAIRS WERE FOUND FOR ATOM LIST
      219 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     -7.63711      0.59918      0.66838      0.00434
MINI INTERN>        0.11369      2.13291      0.00000      0.78626      0.48963
MINI EXTERN>      -11.08940     -0.07020      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220     -7.88852      0.25141      0.44211      0.00244
MINI INTERN>        0.13418      1.95875      0.00000      0.80008      0.37948
MINI EXTERN>      -11.13265     -0.02837      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -7.97325      0.08473      0.61993      0.00382
MINI INTERN>        0.15167      1.98046      0.00000      0.69803      0.44215
MINI EXTERN>      -11.23442     -0.01114      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       245
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1584 ATOM PAIRS WERE FOUND FOR ATOM LIST
      214 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      260     -8.05447      0.08122      0.19621      0.00129
MINI INTERN>        0.14431      2.00666      0.00000      0.64380      0.37895
MINI EXTERN>      -11.27265      0.04446      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -8.09371      0.03924      0.23420      0.00121
MINI INTERN>        0.13799      1.99794      0.00000      0.66615      0.38805
MINI EXTERN>      -11.30863      0.02479      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300     -8.10915      0.01544      0.28559      0.00113
MINI INTERN>        0.13406      1.98023      0.00000      0.64812      0.37339
MINI EXTERN>      -11.28016      0.03521      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      316     -8.12283      0.01367      0.08688      0.00053
ABNR INTERN>        0.14384      1.99309      0.00000      0.60391      0.39110
ABNR EXTERN>      -11.28983      0.03507      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.12283"
 Comparing "-8.12283" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.12283"
 Comparing "-8.12283" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.12283"
 Comparing "-8.12283" and "-9.66664".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.12283"
 Comparing "-8.12283" and "-9.66664".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.388141"
 Parameter: R <- "0.388141"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.12283"
Evaluating: -8.12283--9.66664
 Parameter: DELE <- "1.54381"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "1.54381"
Evaluating: 1.00654*1.54381
 Parameter: BETADELE <- "1.55391"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "1.55391"
Evaluating: EXP(-1.55391)
 Parameter: DELN <- "0.21142"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.21142"
 Parameter: R -> "0.388141"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.21142" and "0.388141".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.21142"
 Parameter: R -> "0.388141"
 Comparing "0.21142" and "0.388141".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "15"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "20"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "15"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "15" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.492179"
 Parameter: CHICHOICE1 <- "0.492179"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.492179"
 Parameter: BONDS -> "5"
Evaluating: INT(0.492179*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 5.819836E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.13988"
 Parameter: CHI <- "0.13988"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.13988"
Evaluating: (0.13988*360)-180.0
 Parameter: CHI2 <- "-129.643"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "-129.643"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1970 ATOM PAIRS WERE FOUND FOR ATOM LIST
      189 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  25324.63282 -25332.75565  20812.43733      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     11.27075      0.04830
MINI EXTERN>    25290.71952      0.59719      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1959 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1919 ATOM PAIRS WERE FOUND FOR ATOM LIST
      184 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1843 ATOM PAIRS WERE FOUND FOR ATOM LIST
      173 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    139.30186  25185.33096     17.95060      0.02311
MINI INTERN>       13.62584     37.22147      0.00000     12.20804      0.65161
MINI EXTERN>       75.46552      0.12939      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1781 ATOM PAIRS WERE FOUND FOR ATOM LIST
      172 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     73.03995     66.26190     11.85139      0.01113
MINI INTERN>        3.37517     24.21418      0.00000     11.98633      0.90344
MINI EXTERN>       32.58107     -0.02024      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1707 ATOM PAIRS WERE FOUND FOR ATOM LIST
      173 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     53.92405     19.11590      5.55713      0.00536
MINI INTERN>        2.78289     19.46752      0.00000     10.14847      1.23089
MINI EXTERN>       20.44770     -0.15342      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     43.20077     10.72328      5.97980      0.00619
MINI INTERN>        2.48476     17.39050      0.00000      7.92631      1.58732
MINI EXTERN>       14.09404     -0.28217      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     36.01898      7.18178      2.75932      0.00298
MINI INTERN>        1.96582     16.17024      0.00000      6.48670      1.88057
MINI EXTERN>        9.89454     -0.37889      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     31.19083      4.82815      2.24661      0.00344
MINI INTERN>        1.77291     15.30545      0.00000      5.63959      2.14696
MINI EXTERN>        6.77833     -0.45241      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       124
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1619 ATOM PAIRS WERE FOUND FOR ATOM LIST
      169 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     27.68404      3.50679      5.27108      0.00398
MINI INTERN>        1.64515     14.79768      0.00000      5.11814      2.32546
MINI EXTERN>        4.30459     -0.50697      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     24.87015      2.81389      1.77021      0.00192
MINI INTERN>        1.54938     14.05884      0.00000      4.79043      2.46391
MINI EXTERN>        2.55104     -0.54344      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     22.79039      2.07976      1.53411      0.00221
MINI INTERN>        1.44759     13.60161      0.00000      4.58014      2.52896
MINI EXTERN>        1.18479     -0.55271      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     20.97165      1.81874      2.03449      0.00256
MINI INTERN>        1.40411     13.11748      0.00000      4.41460      2.57472
MINI EXTERN>       -0.00739     -0.53187      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     20.97165      1.81874      2.03449      0.00307
STPD INTERN>        1.40411     13.11748      0.00000      4.41460      2.57472
STPD EXTERN>       -0.00739     -0.53187      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1619 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1584 ATOM PAIRS WERE FOUND FOR ATOM LIST
      166 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     20.97165      1.81874      2.03449      0.00000
MINI INTERN>        1.40411     13.11748      0.00000      4.41460      2.57472
MINI EXTERN>       -0.00739     -0.53187      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1522 ATOM PAIRS WERE FOUND FOR ATOM LIST
      164 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1469 ATOM PAIRS WERE FOUND FOR ATOM LIST
      164 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1429 ATOM PAIRS WERE FOUND FOR ATOM LIST
      161 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1404 ATOM PAIRS WERE FOUND FOR ATOM LIST
      161 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20      4.68100     16.29066      5.86225      0.04236
MINI INTERN>        0.76471      7.85741      0.00000      3.73338      3.63979
MINI EXTERN>      -11.20613     -0.10816      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1357 ATOM PAIRS WERE FOUND FOR ATOM LIST
      153 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      1.49208      3.18891      2.62674      0.01292
MINI INTERN>        0.28244      4.97542      0.00000      4.62182      1.98567
MINI EXTERN>      -10.41124      0.03797      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        52
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1377 ATOM PAIRS WERE FOUND FOR ATOM LIST
      150 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -0.54411      2.03620      2.37205      0.01212
MINI INTERN>        0.21946      4.44017      0.00000      4.18508      1.95828
MINI EXTERN>      -11.56276      0.21567      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        69
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1380 ATOM PAIRS WERE FOUND FOR ATOM LIST
      151 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        78
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1405 ATOM PAIRS WERE FOUND FOR ATOM LIST
      153 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -3.22868      2.68457      1.98460      0.01137
MINI INTERN>        0.20108      3.45047      0.00000      3.34719      1.21547
MINI EXTERN>      -12.09098      0.64810      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        91
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1430 ATOM PAIRS WERE FOUND FOR ATOM LIST
      154 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -3.98915      0.76048      0.63524      0.00384
MINI INTERN>        0.13761      2.78031      0.00000      3.09095      0.71853
MINI EXTERN>      -11.54105      0.82449      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -4.15058      0.16143      0.73284      0.00360
MINI INTERN>        0.15650      2.72467      0.00000      3.10584      0.59844
MINI EXTERN>      -11.56941      0.83337      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       130
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1451 ATOM PAIRS WERE FOUND FOR ATOM LIST
      156 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     -4.34177      0.19119      0.57345      0.00338
MINI INTERN>        0.15535      2.84939      0.00000      3.02389      0.64639
MINI EXTERN>      -11.82752      0.81072      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       149
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1453 ATOM PAIRS WERE FOUND FOR ATOM LIST
      157 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -4.67579      0.33402      1.16536      0.00451
MINI INTERN>        0.13178      2.75251      0.00000      3.00312      0.68432
MINI EXTERN>      -11.95035      0.70284      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       180
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1476 ATOM PAIRS WERE FOUND FOR ATOM LIST
      166 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     -5.04670      0.37092      1.25667      0.00705
MINI INTERN>        0.10487      2.58475      0.00000      3.31128      0.56134
MINI EXTERN>      -11.80262      0.19368      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -5.28293      0.23623      0.62980      0.00397
MINI INTERN>        0.13122      2.48648      0.00000      3.35234      0.60867
MINI EXTERN>      -11.98190      0.12026      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220     -5.46060      0.17766      0.40003      0.00223
MINI INTERN>        0.11758      2.47281      0.00000      3.35226      0.62376
MINI EXTERN>      -12.10050      0.07350      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -5.66929      0.20870      0.68924      0.00349
MINI INTERN>        0.12240      2.60049      0.00000      3.16724      0.57031
MINI EXTERN>      -12.15335      0.02361      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -5.82483      0.15554      0.35171      0.00197
MINI INTERN>        0.11804      2.46814      0.00000      3.10537      0.56726
MINI EXTERN>      -12.01228     -0.07135      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       264
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1488 ATOM PAIRS WERE FOUND FOR ATOM LIST
      170 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      280     -5.96370      0.13886      1.05663      0.00512
MINI INTERN>        0.10742      2.49584      0.00000      3.06058      0.57132
MINI EXTERN>      -11.93136     -0.26749      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300     -5.99470      0.03100      0.08127      0.00062
MINI INTERN>        0.11787      2.55013      0.00000      3.05182      0.55331
MINI EXTERN>      -12.03062     -0.23721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      300     -5.99470      0.03100      0.08127      0.00093
ABNR INTERN>        0.11787      2.55013      0.00000      3.05182      0.55331
ABNR EXTERN>      -12.03062     -0.23721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.9947"
 Comparing "-5.9947" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-5.9947"
 Comparing "-5.9947" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.9947"
 Comparing "-5.9947" and "-9.66664".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-5.9947"
 Comparing "-5.9947" and "-9.66664".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.971342"
 Parameter: R <- "0.971342"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-5.9947"
Evaluating: -5.9947--9.66664
 Parameter: DELE <- "3.67194"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "3.67194"
Evaluating: 1.00654*3.67194
 Parameter: BETADELE <- "3.69595"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "3.69595"
Evaluating: EXP(-3.69595)
 Parameter: DELN <- "2.482386E-02"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "2.482386E-02"
 Parameter: R -> "0.971342"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "2.482386E-02" and "0.971342".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "2.482386E-02"
 Parameter: R -> "0.971342"
 Comparing "2.482386E-02" and "0.971342".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "16"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "21"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "16"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "16" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.347306"
 Parameter: CHICHOICE1 <- "0.347306"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.347306"
 Parameter: BONDS -> "5"
Evaluating: INT(0.347306*5)
 Parameter: CHICHOICE2 <- "1"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "1"
 Parameter: BONDS -> "5"
 Comparing "1" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "1"
 Parameter: CHICHOICE2 -> "1"
 Comparing "1" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 0.164597
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.380324"
 Parameter: CHI <- "0.380324"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "0.380324"
Evaluating: (0.380324*360)-180.0
 Parameter: CHI1 <- "-43.0834"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "-43.0834"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI1COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1192 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        01104867.78277*************2671252.81497      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.63223      0.04830
MINI EXTERN>  1104834.79164      0.31356      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1183 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1175 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     45.571001104822.21177      7.16794      0.00963
MINI INTERN>        1.59666     13.74517      0.00000      9.13914      0.66799
MINI EXTERN>       20.42179      0.00025      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1146 ATOM PAIRS WERE FOUND FOR ATOM LIST
      124 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     23.80590     21.76510     12.05816      0.01113
MINI INTERN>        2.13450      6.60481      0.00000      7.46389      0.43751
MINI EXTERN>        7.31507     -0.14989      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     12.53731     11.26859      4.34921      0.00536
MINI INTERN>        0.44366      4.60246      0.00000      5.94710      0.29865
MINI EXTERN>        1.47802     -0.23258      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80      6.62621      5.91110      2.52994      0.00258
MINI INTERN>        0.28585      3.11222      0.00000      4.91365      0.22685
MINI EXTERN>       -1.64941     -0.26295      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100      3.07988      3.54632      3.98868      0.00298
MINI INTERN>        0.33568      2.13710      0.00000      4.26731      0.18404
MINI EXTERN>       -3.56347     -0.28078      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      1.15409      1.92579      4.74151      0.00344
MINI INTERN>        0.36504      1.72904      0.00000      3.93604      0.16520
MINI EXTERN>       -4.74692     -0.29431      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       121
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1118 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     -0.27005      1.42414      1.18256      0.00166
MINI INTERN>        0.18282      1.52384      0.00000      3.76571      0.15575
MINI EXTERN>       -5.59417     -0.30399      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -1.25329      0.98324      1.55421      0.00192
MINI INTERN>        0.20457      1.37490      0.00000      3.64283      0.15088
MINI EXTERN>       -6.31201     -0.31446      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -1.90524      0.65196      2.81877      0.00221
MINI INTERN>        0.27712      1.27216      0.00000      3.56464      0.14693
MINI EXTERN>       -6.84139     -0.32470      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -2.52120      0.61596      0.90648      0.00107
MINI INTERN>        0.13890      1.26629      0.00000      3.50072      0.14551
MINI EXTERN>       -7.23585     -0.33676      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -2.52120      0.61596      0.90648      0.00128
STPD INTERN>        0.13890      1.26629      0.00000      3.50072      0.14551
STPD EXTERN>       -7.23585     -0.33676      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1118 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1098 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -2.52120      0.61596      0.90648      0.00000
MINI INTERN>        0.13890      1.26629      0.00000      3.50072      0.14551
MINI EXTERN>       -7.23585     -0.33676      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         5
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1055 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -5.77915      3.25794      1.65468      0.00889
MINI INTERN>        0.24209      1.23390      0.00000      3.11463      0.11106
MINI EXTERN>       -9.80334     -0.67749      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -6.45715      0.67800      0.90582      0.00501
MINI INTERN>        0.10262      0.98346      0.00000      2.90123      0.04203
MINI EXTERN>       -9.80479     -0.68170      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -6.74110      0.28395      0.59269      0.00470
MINI INTERN>        0.13105      0.98703      0.00000      2.63495      0.00888
MINI EXTERN>       -9.84078     -0.66222      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        78
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1069 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -6.95179      0.21069      0.59090      0.00441
MINI INTERN>        0.07492      1.30310      0.00000      2.60832      0.00109
MINI EXTERN>      -10.29383     -0.64539      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -7.18467      0.23289      0.44416      0.00248
MINI INTERN>        0.08105      1.29243      0.00000      2.47759      0.00468
MINI EXTERN>      -10.38217     -0.65826      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -7.32268      0.13801      0.69707      0.00388
MINI INTERN>        0.07997      1.20775      0.00000      2.44260      0.00803
MINI EXTERN>      -10.39957     -0.66146      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       139
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1075 ATOM PAIRS WERE FOUND FOR ATOM LIST
      118 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     -7.57003      0.24735      0.58221      0.00364
MINI INTERN>        0.09619      1.00344      0.00000      2.39606      0.01016
MINI EXTERN>      -10.42257     -0.65330      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -7.71771      0.14768      0.33641      0.00205
MINI INTERN>        0.09055      1.00280      0.00000      2.36808      0.00722
MINI EXTERN>      -10.51606     -0.67030      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -7.81184      0.09412      0.39343      0.00192
MINI INTERN>        0.08691      1.00631      0.00000      2.32698      0.00116
MINI EXTERN>      -10.54994     -0.68326      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -7.98971      0.17788      0.63529      0.00300
MINI INTERN>        0.10840      1.08680      0.00000      2.20378      0.00364
MINI EXTERN>      -10.69560     -0.69674      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       203
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1087 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220     -8.53644      0.54673      0.37233      0.00250
MINI INTERN>        0.09881      1.04201      0.00000      1.89513      0.00196
MINI EXTERN>      -10.81530     -0.75905      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -8.70766      0.17122      0.51120      0.00235
MINI INTERN>        0.08069      0.94333      0.00000      1.88906      0.00994
MINI EXTERN>      -10.83615     -0.79452      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      257     -8.72297      0.01531      0.09977      0.00098
ABNR INTERN>        0.08515      0.92633      0.00000      1.87560      0.00909
ABNR EXTERN>      -10.82608     -0.79306      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.72297"
 Comparing "-8.72297" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.72297"
 Comparing "-8.72297" and "-9.66664".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-9.66664"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-8.72297"
 Comparing "-8.72297" and "-9.66664".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.72297"
 Comparing "-8.72297" and "-9.66664".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.113979"
 Parameter: R <- "0.113979"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-9.66664"
 RDCMND substituted energy or value "?ENER" to "-8.72297"
Evaluating: -8.72297--9.66664
 Parameter: DELE <- "0.94367"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "0.94367"
Evaluating: 1.00654*0.94367
 Parameter: BETADELE <- "0.949841"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "0.949841"
Evaluating: EXP(-0.949841)
 Parameter: DELN <- "0.386803"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.386803"
 Parameter: R -> "0.113979"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.386803" and "0.113979".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.386803"
 Parameter: R -> "0.113979"
 Comparing "0.386803" and "0.113979".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.386803"
 Parameter: R -> "0.113979"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.386803" and "0.113979".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.386803"
 Parameter: R -> "0.113979"
 Comparing "0.386803" and "0.113979".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1059.9057  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.701008
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.70101"
 Parameter: RMSD <- "8.70101"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.70101"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.70101" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.70101"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.70101" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.70101"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.70101" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "6"
 Comparing "2" and "6".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1108.2930  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.897403
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.8974"
 Parameter: RMSD <- "8.8974"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.8974"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.8974" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.8974"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.8974" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.8974"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.8974" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "6"
 Comparing "3" and "6".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1033.0070  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.589890
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.58989"
 Parameter: RMSD <- "8.58989"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.58989"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.58989" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.58989"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.58989" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.58989"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.58989" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "6"
 Comparing "4" and "6".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1471.0814  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.250719
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.2507"
 Parameter: RMSD <- "10.2507"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.2507"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.2507" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.2507"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.2507" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.2507"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.2507" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "6"
 Comparing "5" and "6".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1282.9752  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.572935
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.57294"
 Parameter: RMSD <- "9.57294"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.57294"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.57294" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.57294"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.57294" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.57294"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.57294" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "6"
 Comparing "6" and "6".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "6"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame6.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1098.7634  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.859069
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.85907"
 Parameter: RMSD <- "8.85907"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.85907"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.85907" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.85907"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.85907" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.85907"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.85907" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "7"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "7"
 Parameter: ACCEPTS -> "6"
 Comparing "7" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "8.85907"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "8.85907" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "8.85907"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.85907" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "7"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "7"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "7" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "7"
 Comparing "7" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "7"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "7" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "7"
 Comparing "7" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "7"
 VOPEN> Attempting to open::frames/frame7.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame7.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -8.72297 8.515339E-02 0.926328 1.8756 -10.8261 -0.793059
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-8.72297"
 Parameter: ELAST <- "-8.72297"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "22"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "16"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "16" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.639914"
 Parameter: CHICHOICE1 <- "0.639914"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.639914"
 Parameter: BONDS -> "5"
Evaluating: INT(0.639914*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 3.787344E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.538945"
 Parameter: CHI <- "0.538945"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.538945"
Evaluating: (0.538945*360)-180.0
 Parameter: CHI3 <- "14.0202"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "14.0202"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1180 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   6774.24355  -6782.96652  10581.90467      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.21651      0.04830
MINI EXTERN>     6741.79548      0.18621      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1174 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     20.39489   6753.84866      5.41855      0.00963
MINI INTERN>        0.56795      7.87566      0.00000      7.58197      0.44998
MINI EXTERN>        3.92147     -0.00213      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1154 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      7.75932     12.63557      4.48201      0.00464
MINI INTERN>        0.43213      4.06323      0.00000      5.99409      0.47554
MINI EXTERN>       -3.02600     -0.17967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      2.98091      4.77841      6.46393      0.00536
MINI INTERN>        0.61613      2.97042      0.00000      5.12249      0.36770
MINI EXTERN>       -5.75581     -0.34002      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -0.04502      3.02593      1.56392      0.00258
MINI INTERN>        0.14527      2.52979      0.00000      4.61181      0.26875
MINI EXTERN>       -7.15098     -0.44967      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -1.69074      1.64572      3.94972      0.00298
MINI INTERN>        0.22862      2.25457      0.00000      4.25702      0.19668
MINI EXTERN>       -8.09907     -0.52856      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       104
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1125 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -2.74982      1.05907      4.13216      0.00344
MINI INTERN>        0.24698      2.08370      0.00000      4.02664      0.15129
MINI EXTERN>       -8.68121     -0.57722      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -3.69737      0.94755      1.36514      0.00166
MINI INTERN>        0.13274      1.93545      0.00000      3.85689      0.11997
MINI EXTERN>       -9.13037     -0.61206      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -4.24926      0.55189      2.26439      0.00192
MINI INTERN>        0.15961      1.85230      0.00000      3.71910      0.09843
MINI EXTERN>       -9.44272     -0.63599      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -4.73437      0.48511      0.81953      0.00092
MINI INTERN>        0.09642      1.81136      0.00000      3.59721      0.08273
MINI EXTERN>       -9.66869     -0.65340      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -5.07556      0.34119      0.79680      0.00107
MINI INTERN>        0.09735      1.76714      0.00000      3.50328      0.07148
MINI EXTERN>       -9.85031     -0.66451      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -5.07556      0.34119      0.79680      0.00128
STPD INTERN>        0.09735      1.76714      0.00000      3.50328      0.07148
STPD EXTERN>       -9.85031     -0.66451      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1125 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1106 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -5.07556      0.34119      0.79680      0.00000
MINI INTERN>        0.09735      1.76714      0.00000      3.50328      0.07148
MINI EXTERN>       -9.85031     -0.66451      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20     -6.59211      1.51655      0.83244      0.00417
MINI INTERN>        0.09078      1.77556      0.00000      2.85761      0.01506
MINI EXTERN>      -10.70736     -0.62375      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        25
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1069 ATOM PAIRS WERE FOUND FOR ATOM LIST
      113 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -6.96639      0.37428      0.79505      0.00391
MINI INTERN>        0.09362      1.60692      0.00000      2.81278      0.04179
MINI EXTERN>      -10.84594     -0.67556      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1070 ATOM PAIRS WERE FOUND FOR ATOM LIST
      115 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -7.40253      0.43614      1.03987      0.00612
MINI INTERN>        0.11180      2.08137      0.00000      2.24365      0.02530
MINI EXTERN>      -11.15800     -0.70665      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1083 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -8.61252      1.21000      2.07922      0.01007
MINI INTERN>        0.12529      1.39585      0.00000      1.20139      0.00266
MINI EXTERN>      -10.71288     -0.62484      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -8.95059      0.33807      1.03646      0.00567
MINI INTERN>        0.12796      1.32008      0.00000      1.08697      0.00300
MINI EXTERN>      -10.81501     -0.67359      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       107
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1074 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -9.25459      0.30400      0.57262      0.00319
MINI INTERN>        0.10279      1.34419      0.00000      1.12107      0.01751
MINI EXTERN>      -11.08195     -0.75820      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       124
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1094 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       133
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1118 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       134
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1103 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     -9.71675      0.46216      1.47867      0.00739
MINI INTERN>        0.18572      1.10571      0.00000      1.03932      0.04611
MINI EXTERN>      -10.87202     -1.22159      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       143
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1125 ATOM PAIRS WERE FOUND FOR ATOM LIST
      123 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       148
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1101 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       151
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1115 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160    -10.55410      0.83735      1.11511      0.00548
MINI INTERN>        0.09554      0.91762      0.00000      1.27421      0.07568
MINI EXTERN>      -11.62652     -1.29062      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180    -10.81395      0.25985      0.61666      0.00308
MINI INTERN>        0.09969      0.90699      0.00000      1.22140      0.05141
MINI EXTERN>      -11.68651     -1.40693      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200    -10.97300      0.15906      0.41386      0.00289
MINI INTERN>        0.07955      0.90885      0.00000      1.22788      0.03757
MINI EXTERN>      -11.75874     -1.46811      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       213
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1133 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220    -11.21224      0.23924      0.31372      0.00163
MINI INTERN>        0.09746      0.97718      0.00000      1.27142      0.00202
MINI EXTERN>      -11.94982     -1.61051      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240    -11.25797      0.04573      0.12462      0.00092
MINI INTERN>        0.09139      0.93415      0.00000      1.29078      0.00188
MINI EXTERN>      -11.98649     -1.58968      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      255    -11.27221      0.01425      0.08429      0.00047
ABNR INTERN>        0.08486      0.90521      0.00000      1.28528      0.00327
ABNR EXTERN>      -11.99108     -1.55976      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-8.72297"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-11.2722"
 Comparing "-11.2722" and "-8.72297".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-8.72297"
 RDCMND substituted energy or value "?ENER" to "-11.2722"
 Comparing "-11.2722" and "-8.72297".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    948.1351  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.229455
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.22946"
 Parameter: RMSD <- "8.22946"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.22946"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.22946" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.22946"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.22946" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.22946"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.22946" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "7"
 Comparing "2" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1067.1782  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.730809
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.73081"
 Parameter: RMSD <- "8.73081"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.73081"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.73081" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.73081"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.73081" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.73081"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.73081" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "7"
 Comparing "3" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1123.9473  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.960020
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.96002"
 Parameter: RMSD <- "8.96002"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.96002"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.96002" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.96002"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.96002" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.96002"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.96002" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "7"
 Comparing "4" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1565.1948  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.573534
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.5735"
 Parameter: RMSD <- "10.5735"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.5735"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.5735" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.5735"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.5735" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.5735"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.5735" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "7"
 Comparing "5" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1376.5825  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.916013
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.91601"
 Parameter: RMSD <- "9.91601"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.91601"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.91601" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.91601"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.91601" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.91601"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.91601" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "7"
 Comparing "6" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "6"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame6.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1127.9886  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.976114
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.97611"
 Parameter: RMSD <- "8.97611"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.97611"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.97611" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.97611"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.97611" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.97611"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.97611" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "7"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "7"
 Parameter: ACCEPTS -> "7"
 Comparing "7" and "7".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "7"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame7.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame7.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS     23.2110  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    1.287606
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "1.28761"
 Parameter: RMSD <- "1.28761"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "1.28761"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.28761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "1.28761"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.28761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "1.28761"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.28761" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "8"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "8"
 Parameter: ACCEPTS -> "7"
 Comparing "8" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-8.72297"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-11.2722"
 Comparing "-11.2722" and "-8.72297".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-8.72297"
 RDCMND substituted energy or value "?ENER" to "-11.2722"
 Comparing "-11.2722" and "-8.72297".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "1.28761"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1.28761" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "1.28761"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.28761" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "8"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "8"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "8" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "8"
 Comparing "8" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "8"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "8" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "8"
 Comparing "8" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "8"
 VOPEN> Attempting to open::frames/frame8.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame8.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -11.2722 8.486222E-02 0.905214 1.28528 -11.9911 -1.55976
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-11.2722"
 Parameter: ELAST <- "-11.2722"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "23"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "16"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "16" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "4.485731E-02"
 Parameter: CHICHOICE1 <- "4.485731E-02"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "4.485731E-02"
 Parameter: BONDS -> "5"
Evaluating: INT(4.485731E-02*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.916749
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.802377"
 Parameter: CHI <- "0.802377"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.802377"
Evaluating: (0.802377*360)-180.0
 Parameter: CHI5 <- "108.856"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "108.856"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1140 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0    470.09858   -481.37080    355.31806      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.21651      0.04830
MINI EXTERN>      438.01155     -0.17482      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1135 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     23.50905    446.58953      6.93389      0.00963
MINI INTERN>        0.43558      7.17027      0.00000      8.89321      0.18128
MINI EXTERN>        7.19936     -0.37064      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1107 ATOM PAIRS WERE FOUND FOR ATOM LIST
      123 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     11.35630     12.15276      2.97299      0.00464
MINI INTERN>        0.07547      3.60737      0.00000      8.26061      0.14469
MINI EXTERN>       -0.27774     -0.45412      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      6.34654      5.00975      6.72497      0.00536
MINI INTERN>        0.33909      2.68897      0.00000      7.44840      0.07314
MINI EXTERN>       -3.68262     -0.52043      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80      3.21512      3.13143      1.61837      0.00258
MINI INTERN>        0.06198      2.14993      0.00000      6.81982      0.04449
MINI EXTERN>       -5.30077     -0.56033      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        99
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1080 ATOM PAIRS WERE FOUND FOR ATOM LIST
      117 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100      1.45882      1.75630      3.88999      0.00298
MINI INTERN>        0.19758      1.94406      0.00000      6.28625      0.03661
MINI EXTERN>       -6.42049     -0.58519      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      0.35160      1.10722      4.26279      0.00344
MINI INTERN>        0.23419      1.84137      0.00000      5.92861      0.03617
MINI EXTERN>       -7.08975     -0.59899      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -0.63479      0.98639      1.99685      0.00166
MINI INTERN>        0.09046      1.79907      0.00000      5.62074      0.03817
MINI EXTERN>       -7.57351     -0.60973      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -1.25820      0.62341      2.39738      0.00192
MINI INTERN>        0.11280      1.73119      0.00000      5.40121      0.03692
MINI EXTERN>       -7.92284     -0.61748      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -1.71899      0.46079      2.66689      0.00221
MINI INTERN>        0.13177      1.67895      0.00000      5.23102      0.03428
MINI EXTERN>       -8.17173     -0.62330      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -2.16655      0.44756      0.64985      0.00107
MINI INTERN>        0.08677      1.61838      0.00000      5.09663      0.02946
MINI EXTERN>       -8.36986     -0.62792      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -2.16655      0.44756      0.64985      0.00128
STPD INTERN>        0.08677      1.61838      0.00000      5.09663      0.02946
STPD EXTERN>       -8.36986     -0.62792      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1080 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1057 ATOM PAIRS WERE FOUND FOR ATOM LIST
      113 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -2.16655      0.44756      0.64985      0.00000
MINI INTERN>        0.08677      1.61838      0.00000      5.09663      0.02946
MINI EXTERN>       -8.36986     -0.62792      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      112 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -4.26382      2.09727      1.13293      0.00474
MINI INTERN>        0.12963      1.53512      0.00000      3.84904      0.00011
MINI EXTERN>       -9.18942     -0.58831      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     -4.33322      0.06940      0.31633      0.00160
MINI INTERN>        0.10053      1.52035      0.00000      3.80603      0.00096
MINI EXTERN>       -9.19141     -0.56968      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -4.40847      0.07525      0.40004      0.00250
MINI INTERN>        0.11825      1.47633      0.00000      3.73409      0.00543
MINI EXTERN>       -9.20113     -0.54145      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>       77     -4.43239      0.02392      0.09779      0.00104
ABNR INTERN>        0.10567      1.48710      0.00000      3.74177      0.00493
ABNR EXTERN>       -9.23033     -0.54152      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-4.43239"
 Comparing "-4.43239" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.43239"
 Comparing "-4.43239" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-4.43239"
 Comparing "-4.43239" and "-11.2722".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.43239"
 Comparing "-4.43239" and "-11.2722".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.548015"
 Parameter: R <- "0.548015"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.43239"
Evaluating: -4.43239--11.2722
 Parameter: DELE <- "6.83981"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "6.83981"
Evaluating: 1.00654*6.83981
 Parameter: BETADELE <- "6.88454"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "6.88454"
Evaluating: EXP(-6.88454)
 Parameter: DELN <- "1.023487E-03"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "1.023487E-03"
 Parameter: R -> "0.548015"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1.023487E-03" and "0.548015".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "1.023487E-03"
 Parameter: R -> "0.548015"
 Comparing "1.023487E-03" and "0.548015".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "17"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "24"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "17"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "17" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.48003"
 Parameter: CHICHOICE1 <- "0.48003"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.48003"
 Parameter: BONDS -> "5"
Evaluating: INT(0.48003*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.858637
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.113435"
 Parameter: CHI <- "0.113435"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.113435"
Evaluating: (0.113435*360)-180.0
 Parameter: CHI2 <- "-139.163"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "-139.163"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1116 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     52.85889    -57.29128     42.73531      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.61336      0.04830
MINI EXTERN>       20.57694     -0.37676      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20      9.06594     43.79296      5.02984      0.00401
MINI INTERN>        0.36337      2.47020      0.00000      8.91427      0.08051
MINI EXTERN>       -2.11820     -0.64421      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40      6.00272      3.06322      5.93453      0.00464
MINI INTERN>        0.44379      1.90311      0.00000      8.43368      0.07365
MINI EXTERN>       -4.11747     -0.73404      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      3.83220      2.17052      1.40660      0.00223
MINI INTERN>        0.08834      1.82352      0.00000      7.94274      0.05637
MINI EXTERN>       -5.28697     -0.79178      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1096 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80      2.52616      1.30604      3.46924      0.00258
MINI INTERN>        0.12704      1.82631      0.00000      7.47260      0.04305
MINI EXTERN>       -6.11088     -0.83195      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100      1.61689      0.90927      3.79399      0.00298
MINI INTERN>        0.15005      1.79040      0.00000      7.12977      0.03625
MINI EXTERN>       -6.63568     -0.85390      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      0.77250      0.84439      0.89728      0.00144
MINI INTERN>        0.09740      1.66942      0.00000      6.86867      0.03239
MINI EXTERN>       -7.02966     -0.86571      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      0.20732      0.56518      2.05478      0.00166
MINI INTERN>        0.13616      1.60968      0.00000      6.64961      0.03003
MINI EXTERN>       -7.34502     -0.87314      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -0.24728      0.45460      2.35960      0.00192
MINI INTERN>        0.14899      1.56481      0.00000      6.47299      0.02820
MINI EXTERN>       -7.58440     -0.87785      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -0.66832      0.42104      0.89206      0.00092
MINI INTERN>        0.09878      1.53858      0.00000      6.32076      0.02607
MINI EXTERN>       -7.76988     -0.88262      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -0.98461      0.31629      0.78125      0.00107
MINI INTERN>        0.09941      1.50213      0.00000      6.19613      0.02417
MINI EXTERN>       -7.92228     -0.88417      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -0.98461      0.31629      0.78125      0.00128
STPD INTERN>        0.09941      1.50213      0.00000      6.19613      0.02417
STPD EXTERN>       -7.92228     -0.88417      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1096 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1071 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -0.98461      0.31629      0.78125      0.00000
MINI INTERN>        0.09941      1.50213      0.00000      6.19613      0.02417
MINI EXTERN>       -7.92228     -0.88417      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1043 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -2.93179      1.94718      1.23386      0.00463
MINI INTERN>        0.09856      1.56943      0.00000      5.05682      0.00348
MINI EXTERN>       -8.82007     -0.84001      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     -3.18255      0.25076      0.90840      0.00435
MINI INTERN>        0.11398      1.74873      0.00000      4.57503      0.01548
MINI EXTERN>       -8.72955     -0.90621      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1047 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -3.46031      0.27776      1.35235      0.00679
MINI INTERN>        0.12317      1.85515      0.00000      3.83857      0.03978
MINI EXTERN>       -8.40981     -0.90716      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        69
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -3.71718      0.25687      0.39413      0.00229
MINI INTERN>        0.10466      1.67637      0.00000      3.43704      0.02340
MINI EXTERN>       -8.07204     -0.88660      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -3.94878      0.23160      0.36259      0.00215
MINI INTERN>        0.12762      1.38350      0.00000      3.23908      0.00619
MINI EXTERN>       -7.88842     -0.81675      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -3.98131      0.03253      0.34782      0.00202
MINI INTERN>        0.11881      1.38203      0.00000      3.20545      0.00459
MINI EXTERN>       -7.88441     -0.80776      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      136     -4.01271      0.03140      0.07886      0.00056
ABNR INTERN>        0.12129      1.39900      0.00000      3.14789      0.00386
ABNR EXTERN>       -7.89381     -0.79093      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-4.01271"
 Comparing "-4.01271" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.01271"
 Comparing "-4.01271" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-4.01271"
 Comparing "-4.01271" and "-11.2722".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.01271"
 Comparing "-4.01271" and "-11.2722".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.498754"
 Parameter: R <- "0.498754"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-4.01271"
Evaluating: -4.01271--11.2722
 Parameter: DELE <- "7.25949"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "7.25949"
Evaluating: 1.00654*7.25949
 Parameter: BETADELE <- "7.30697"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "7.30697"
Evaluating: EXP(-7.30697)
 Parameter: DELN <- "6.708466E-04"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "6.708466E-04"
 Parameter: R -> "0.498754"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6.708466E-04" and "0.498754".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "6.708466E-04"
 Parameter: R -> "0.498754"
 Comparing "6.708466E-04" and "0.498754".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "18"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "25"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "18"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "18" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.559011"
 Parameter: CHICHOICE1 <- "0.559011"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.559011"
 Parameter: BONDS -> "5"
Evaluating: INT(0.559011*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.300648
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.984021"
 Parameter: CHI <- "0.984021"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.984021"
Evaluating: (0.984021*360)-180.0
 Parameter: CHI2 <- "174.248"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "174.248"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1171 ATOM PAIRS WERE FOUND FOR ATOM LIST
      157 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     30.82770    -34.84041     36.22963      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     11.61549      0.04830
MINI EXTERN>       -2.86560      0.03246      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20      4.92393     25.90377      5.13064      0.00401
MINI INTERN>        0.46717      1.85156      0.00000      9.17667      0.00055
MINI EXTERN>       -6.29718     -0.27484      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1167 ATOM PAIRS WERE FOUND FOR ATOM LIST
      160 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      3.13771      1.78621      1.15578      0.00193
MINI INTERN>        0.15653      1.60005      0.00000      8.41221      0.00212
MINI EXTERN>       -6.69985     -0.33335      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      2.29858      0.83913      2.68215      0.00223
MINI INTERN>        0.19357      1.60142      0.00000      7.81690      0.00796
MINI EXTERN>       -6.95475     -0.36651      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80      1.70154      0.59704      0.91222      0.00107
MINI INTERN>        0.15526      1.64314      0.00000      7.40753      0.01530
MINI EXTERN>       -7.13365     -0.38604      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100      1.31929      0.38225      0.97283      0.00124
MINI INTERN>        0.15178      1.72867      0.00000      7.08764      0.02038
MINI EXTERN>       -7.26247     -0.40672      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      1.05868      0.26060      1.71895      0.00144
MINI INTERN>        0.17017      1.80587      0.00000      6.85125      0.02311
MINI EXTERN>       -7.36428     -0.42743      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      0.84314      0.21554      2.15439      0.00166
MINI INTERN>        0.15751      1.89950      0.00000      6.65746      0.02377
MINI EXTERN>       -7.44484     -0.45026      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160      0.62394      0.21920      0.93047      0.00080
MINI INTERN>        0.15728      1.94440      0.00000      6.49150      0.02255
MINI EXTERN>       -7.51751     -0.47428      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180      0.46631      0.15763      1.14993      0.00092
MINI INTERN>        0.16919      1.99892      0.00000      6.35330      0.02131
MINI EXTERN>       -7.58080     -0.49560      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      0.32249      0.14382      0.40670      0.00044
MINI INTERN>        0.14667      2.05701      0.00000      6.24383      0.02014
MINI EXTERN>       -7.63158     -0.51358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      0.32249      0.14382      0.40670      0.00053
STPD INTERN>        0.14667      2.05701      0.00000      6.24383      0.02014
STPD EXTERN>       -7.63158     -0.51358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1167 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1157 ATOM PAIRS WERE FOUND FOR ATOM LIST
      154 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      0.32249      0.14382      0.40670      0.00000
MINI INTERN>        0.14667      2.05701      0.00000      6.24383      0.02014
MINI EXTERN>       -7.63158     -0.51358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20     -1.04533      1.36782      1.21758      0.00593
MINI INTERN>        0.15301      2.83630      0.00000      4.84590      0.01479
MINI EXTERN>       -8.09980     -0.79554      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1210 ATOM PAIRS WERE FOUND FOR ATOM LIST
      165 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -1.91029      0.86496      1.30852      0.00927
MINI INTERN>        0.17515      3.53842      0.00000      3.49769      0.03697
MINI EXTERN>       -8.29784     -0.86068      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60     -2.23999      0.32970      0.53011      0.00313
MINI INTERN>        0.13854      3.17778      0.00000      3.55806      0.01862
MINI EXTERN>       -8.29247     -0.84052      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -2.47080      0.23081      0.25259      0.00176
MINI INTERN>        0.12928      2.54551      0.00000      4.06017      0.00758
MINI EXTERN>       -8.41005     -0.80329      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -2.77893      0.30813      0.45581      0.00276
MINI INTERN>        0.12831      2.14053      0.00000      3.92458      0.00733
MINI EXTERN>       -8.20747     -0.77222      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       117
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1259 ATOM PAIRS WERE FOUND FOR ATOM LIST
      163 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -2.81184      0.03291      0.30726      0.00155
MINI INTERN>        0.12520      2.17953      0.00000      3.92601      0.00792
MINI EXTERN>       -8.27306     -0.77744      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -2.88328      0.07144      0.79501      0.00404
MINI INTERN>        0.10593      2.24040      0.00000      3.80752      0.01666
MINI EXTERN>       -8.26165     -0.79214      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -3.11245      0.22918      0.36528      0.00227
MINI INTERN>        0.13251      2.13113      0.00000      3.14120      0.01305
MINI EXTERN>       -7.73220     -0.79813      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -3.27404      0.16159      0.44105      0.00213
MINI INTERN>        0.12520      2.19403      0.00000      3.07940      0.00680
MINI EXTERN>       -7.86180     -0.81766      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -3.30342      0.02938      0.45166      0.00200
MINI INTERN>        0.11671      2.19652      0.00000      3.03848      0.00459
MINI EXTERN>       -7.84801     -0.81171      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       215
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1239 ATOM PAIRS WERE FOUND FOR ATOM LIST
      165 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220     -3.34625      0.04282      0.40569      0.00188
MINI INTERN>        0.11998      1.96133      0.00000      3.12305      0.01018
MINI EXTERN>       -7.76594     -0.79485      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -3.37436      0.02812      0.21210      0.00106
MINI INTERN>        0.11763      2.07603      0.00000      3.02376      0.01012
MINI EXTERN>       -7.79960     -0.80230      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -3.45354      0.07917      0.49272      0.00275
MINI INTERN>        0.13656      1.96111      0.00000      2.74066      0.01679
MINI EXTERN>       -7.53964     -0.76902      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -3.56735      0.11381      0.25936      0.00155
MINI INTERN>        0.12760      1.74683      0.00000      2.65508      0.01215
MINI EXTERN>       -7.36216     -0.74685      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      296     -3.57899      0.01165      0.09601      0.00043
ABNR INTERN>        0.12673      1.73336      0.00000      2.63767      0.01334
ABNR EXTERN>       -7.34550     -0.74460      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-3.57899"
 Comparing "-3.57899" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-3.57899"
 Comparing "-3.57899" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-3.57899"
 Comparing "-3.57899" and "-11.2722".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-3.57899"
 Comparing "-3.57899" and "-11.2722".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.447288"
 Parameter: R <- "0.447288"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-3.57899"
Evaluating: -3.57899--11.2722
 Parameter: DELE <- "7.69321"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "7.69321"
Evaluating: 1.00654*7.69321
 Parameter: BETADELE <- "7.74352"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "7.74352"
Evaluating: EXP(-7.74352)
 Parameter: DELN <- "4.335429E-04"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "4.335429E-04"
 Parameter: R -> "0.447288"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "4.335429E-04" and "0.447288".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "4.335429E-04"
 Parameter: R -> "0.447288"
 Comparing "4.335429E-04" and "0.447288".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "19"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "26"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "19"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "19" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.567542"
 Parameter: CHICHOICE1 <- "0.567542"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.567542"
 Parameter: BONDS -> "5"
Evaluating: INT(0.567542*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.671499
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.885051"
 Parameter: CHI <- "0.885051"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.885051"
Evaluating: (0.885051*360)-180.0
 Parameter: CHI2 <- "138.618"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "138.618"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1635 ATOM PAIRS WERE FOUND FOR ATOM LIST
      230 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0   5185.18379  -5188.76279   4883.13152      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.59075      0.04830
MINI EXTERN>     5152.07816      0.46954      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1618 ATOM PAIRS WERE FOUND FOR ATOM LIST
      222 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1557 ATOM PAIRS WERE FOUND FOR ATOM LIST
      207 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     76.98778   5108.19601     28.82124      0.02311
MINI INTERN>       11.66837     20.27115      0.00000      9.43447      0.66127
MINI EXTERN>       35.05933     -0.10682      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     35.64264     41.34514     13.98638      0.01113
MINI INTERN>        3.17723      9.09311      0.00000      7.96165      1.03268
MINI EXTERN>       14.81180     -0.43384      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        44
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1513 ATOM PAIRS WERE FOUND FOR ATOM LIST
      205 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     20.22359     15.41904      5.51577      0.00536
MINI INTERN>        1.05023      6.14057      0.00000      7.15033      0.92976
MINI EXTERN>        5.48614     -0.53344      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     13.63438      6.58921      8.26718      0.00619
MINI INTERN>        1.10264      5.10620      0.00000      6.57656      0.74986
MINI EXTERN>        0.63621     -0.53709      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        88
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1460 ATOM PAIRS WERE FOUND FOR ATOM LIST
      205 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100      9.30042      4.33397      3.11149      0.00298
MINI INTERN>        0.37624      4.77261      0.00000      6.09424      0.60205
MINI EXTERN>       -2.02436     -0.52036      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      6.99175      2.30866      4.12781      0.00344
MINI INTERN>        0.36668      4.65484      0.00000      5.70595      0.49063
MINI EXTERN>       -3.71996     -0.50639      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140      5.46349      1.52826      4.89523      0.00398
MINI INTERN>        0.37818      4.63940      0.00000      5.38606      0.41051
MINI EXTERN>       -4.85339     -0.49726      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160      4.14319      1.32030      2.32842      0.00192
MINI INTERN>        0.25644      4.57635      0.00000      5.14225      0.34948
MINI EXTERN>       -5.68892     -0.49240      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180      3.30759      0.83560      2.84265      0.00221
MINI INTERN>        0.28394      4.57870      0.00000      4.92745      0.30526
MINI EXTERN>       -6.29354     -0.49422      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      2.68705      0.62054      3.24565      0.00256
MINI INTERN>        0.31472      4.57949      0.00000      4.75719      0.27362
MINI EXTERN>       -6.73765     -0.50031      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      2.68705      0.62054      3.24565      0.00128
STPD INTERN>        0.31472      4.57949      0.00000      4.75719      0.27362
STPD EXTERN>       -6.73765     -0.50031      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1460 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1416 ATOM PAIRS WERE FOUND FOR ATOM LIST
      199 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      2.68150      0.00555      2.64478      0.00000
MINI INTERN>        0.17300      4.68148      0.00000      4.75238      0.27009
MINI EXTERN>       -6.69289     -0.50256      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1370 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -1.33839      4.01989      1.12423      0.00600
MINI INTERN>        0.19120      5.05573      0.00000      3.36698      0.11248
MINI EXTERN>       -9.30023     -0.76454      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     -2.32626      0.98787      2.01470      0.00939
MINI INTERN>        0.12196      3.47754      0.00000      3.86876      0.00508
MINI EXTERN>       -9.10264     -0.69695      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1363 ATOM PAIRS WERE FOUND FOR ATOM LIST
      192 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -2.90798      0.58172      0.96231      0.00528
MINI INTERN>        0.11710      2.69228      0.00000      4.47536      0.00357
MINI EXTERN>       -9.39444     -0.80184      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -3.11992      0.21194      0.40548      0.00297
MINI INTERN>        0.10602      2.97311      0.00000      3.89971      0.00318
MINI EXTERN>       -9.29185     -0.81010      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        94
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1344 ATOM PAIRS WERE FOUND FOR ATOM LIST
      187 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -3.33035      0.21044      0.51853      0.00279
MINI INTERN>        0.09579      2.58149      0.00000      3.82447      0.00661
MINI EXTERN>       -9.07077     -0.76794      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -3.37969      0.04934      0.27964      0.00157
MINI INTERN>        0.08774      2.70177      0.00000      3.75410      0.00361
MINI EXTERN>       -9.15087     -0.77604      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -3.44562      0.06593      0.25964      0.00147
MINI INTERN>        0.08695      2.50730      0.00000      3.90621      0.00540
MINI EXTERN>       -9.16354     -0.78794      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       156
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1321 ATOM PAIRS WERE FOUND FOR ATOM LIST
      187 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -3.60863      0.16301      0.78905      0.00384
MINI INTERN>        0.12905      2.49574      0.00000      3.53364      0.00400
MINI EXTERN>       -9.02478     -0.74628      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -3.75832      0.14969      0.54612      0.00360
MINI INTERN>        0.11347      2.63346      0.00000      3.19060      0.00212
MINI EXTERN>       -8.97277     -0.72521      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       184
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1304 ATOM PAIRS WERE FOUND FOR ATOM LIST
      187 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       195
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1303 ATOM PAIRS WERE FOUND FOR ATOM LIST
      184 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     -4.01738      0.25906      0.54444      0.00338
MINI INTERN>        0.12389      2.89494      0.00000      2.22295      0.00150
MINI EXTERN>       -8.72352     -0.53715      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       207
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1289 ATOM PAIRS WERE FOUND FOR ATOM LIST
      184 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       220
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1299 ATOM PAIRS WERE FOUND FOR ATOM LIST
      189 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220     -3.67852     -0.33886      5.95604      0.00317
MINI INTERN>        0.81369      2.38666      0.00000      2.22424      0.00059
MINI EXTERN>       -8.81144     -0.29226      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       225
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1293 ATOM PAIRS WERE FOUND FOR ATOM LIST
      184 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       228
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1300 ATOM PAIRS WERE FOUND FOR ATOM LIST
      188 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      240     -4.39599      0.71747      1.84461      0.00725
MINI INTERN>        0.22387      1.95867      0.00000      2.10027      0.03174
MINI EXTERN>       -8.37858     -0.33196      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       255
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1303 ATOM PAIRS WERE FOUND FOR ATOM LIST
      186 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      260     -4.79154      0.39555      0.76446      0.00408
MINI INTERN>        0.08777      1.85755      0.00000      2.19845      0.01789
MINI EXTERN>       -8.60830     -0.34489      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -5.00613      0.21459      0.77114      0.00383
MINI INTERN>        0.09319      1.80365      0.00000      2.03023      0.01094
MINI EXTERN>       -8.45556     -0.48859      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      300     -5.09955      0.09342      0.26911      0.00215
MINI INTERN>        0.09024      1.98245      0.00000      2.01479      0.00776
MINI EXTERN>       -8.64811     -0.54668      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      320     -5.31097      0.21142      0.61465      0.00337
MINI INTERN>        0.09296      2.36655      0.00000      1.52204      0.01302
MINI EXTERN>       -8.49777     -0.80776      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       328
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1325 ATOM PAIRS WERE FOUND FOR ATOM LIST
      186 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      340     -5.43985      0.12888      0.34489      0.00190
MINI INTERN>        0.08274      2.12261      0.00000      1.71368      0.00081
MINI EXTERN>       -8.48929     -0.87039      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      360     -5.47902      0.03917      0.39880      0.00178
MINI INTERN>        0.09090      2.11265      0.00000      1.68176      0.00195
MINI EXTERN>       -8.48217     -0.88411      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      380     -5.50163      0.02261      0.11171      0.00060
MINI INTERN>        0.09260      2.09408      0.00000      1.66575      0.00307
MINI EXTERN>       -8.46481     -0.89233      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      400     -5.62073      0.11910      0.25286      0.00157
MINI INTERN>        0.09456      1.89022      0.00000      1.73200      0.00857
MINI EXTERN>       -8.40388     -0.94219      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      420     -5.64412      0.02339      0.16002      0.00088
MINI INTERN>        0.09457      1.79780      0.00000      1.69820      0.00947
MINI EXTERN>       -8.32811     -0.91605      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      423     -5.64539      0.00126      0.08615      0.00058
ABNR INTERN>        0.09247      1.79856      0.00000      1.69613      0.00933
ABNR EXTERN>       -8.32890     -0.91297      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.64539"
 Comparing "-5.64539" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-5.64539"
 Comparing "-5.64539" and "-11.2722".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-11.2722"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.64539"
 Comparing "-5.64539" and "-11.2722".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-5.64539"
 Comparing "-5.64539" and "-11.2722".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "5.310195E-02"
 Parameter: R <- "5.310195E-02"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-11.2722"
 RDCMND substituted energy or value "?ENER" to "-5.64539"
Evaluating: -5.64539--11.2722
 Parameter: DELE <- "5.62681"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "5.62681"
Evaluating: 1.00654*5.62681
 Parameter: BETADELE <- "5.66361"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "5.66361"
Evaluating: EXP(-5.66361)
 Parameter: DELN <- "3.469968E-03"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "3.469968E-03"
 Parameter: R -> "5.310195E-02"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3.469968E-03" and "5.310195E-02".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "3.469968E-03"
 Parameter: R -> "5.310195E-02"
 Comparing "3.469968E-03" and "5.310195E-02".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "20"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "27"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "20"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "20" and "20".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement sims by 1
 Parameter: SIMS <- "2"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   19 with status "KEEP"

                    RETURNING TO INPUT STREAM     5
  
 CHARMM>    IF @sims .LE. @maxsims THEN GOTO mainloop
 Parameter: SIMS -> "2"
 Parameter: MAXSIMS -> "1000"
 Comparing "2" and "1000".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 19 CARD NAME $SL_MOD/charmm/charmm_mmcm_str/mmcm.str
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mmcm.str::
 OPNLGU> Unit 19 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mmcm.str
  
 CHARMM>    STREAM UNIT 19

                    INPUT STREAM SWITCHING TO UNIT    19
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chng change
 Parameter: CHNG <- "CHANGE"
  
 CHARMM>    SET seed1 ?RAND
 RDCMND substituted energy or value "?RAND" to "0.48444"
 Parameter: SEED1 <- "0.48444"
  
 CHARMM>    CALC seed2 = int(@seed1 * 1000000)
 Parameter: SEED1 -> "0.48444"
Evaluating: INT(0.48444*1000000)
 Parameter: SEED2 <- "484440"
  
 CHARMM>    RANDom UNIForm ISEED @seed2
 Parameter: SEED2 -> "484440"
DIST= UNIF     SEED=     484440     SIGMA=    1.000    
    SCALE=    1.000         OFFSET=   0.0000E+00
  
 CHARMM>    SET iterations 0         ! set counter for number of iterations
 Parameter: ITERATIONS <- "0"
  
 CHARMM>    SET dups 0               ! set counter for counting continuous string of duplicates
 Parameter: DUPS <- "0"
  
 CHARMM>    SET rejects 0            ! set number of rejects counter
 Parameter: REJECTS <- "0"
  
 CHARMM>    SET chichoice 0          ! set chi angle choice flag
 Parameter: CHICHOICE <- "0"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    ! generate a starting structure by performing a random rotation around
 CHARMM>    ! each bond tethering the SL to the cys
 CHARMM>     
  
 CHARMM>    SET ntors 1                  ! set chi looping variable
 Parameter: NTORS <- "1"
  
 CHARMM>    LABEL startloop
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "1"
 Parameter: CHICHOICE <- "1"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "1"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "1"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "1"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "1"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "1"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 0.791406
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.166088"
 Parameter: CHI <- "0.166088"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "0.166088"
Evaluating: (0.166088*360)-180.0
 Parameter: CHI1 <- "-120.208"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "-120.208"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "2"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "2"
 Parameter: CHICHOICE <- "2"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "2"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "2"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "2"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "2"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "2"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.442284
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.469909"
 Parameter: CHI <- "0.469909"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.469909"
Evaluating: (0.469909*360)-180.0
 Parameter: CHI2 <- "-10.8327"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "-10.8327"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "3"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "3"
 Parameter: CHICHOICE <- "3"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "3"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "3"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "3"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "3"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "3"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.760492
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.588225"
 Parameter: CHI <- "0.588225"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.588225"
Evaluating: (0.588225*360)-180.0
 Parameter: CHI3 <- "31.761"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "31.761"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "4"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "4"
 Parameter: CHICHOICE <- "4"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "4"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "4"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "4"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "4"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "4"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.293879
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.22344"
 Parameter: CHI <- "0.22344"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.22344"
Evaluating: (0.22344*360)-180.0
 Parameter: CHI4 <- "-99.5616"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "-99.5616"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "5"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "5"
 Parameter: BONDS -> "5"
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
  
 CHARMM>    SET chichoice @ntors
 Parameter: NTORS -> "5"
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN OPEN READ UNIT 2@ntors CARD NAME @strpath/randchi@ntors.str
 Parameter: NTORS -> "5"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "5"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Parameter: NTORS -> "5"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF chi@ntors@chng .EQ. 1 THEN STREAM UNIT 2@ntors
 Parameter: NTORS -> "5"
 Parameter: CHNG -> "CHANGE"
 Parameter: NTORS -> "5"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.350843
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.62651"
 Parameter: CHI <- "0.62651"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.62651"
Evaluating: (0.62651*360)-180.0
 Parameter: CHI5 <- "45.5436"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "45.5436"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    INCRement ntors by 1
 Parameter: NTORS <- "6"
  
 CHARMM>    IF @ntors .LE. @bonds THEN GOTO startloop
 Parameter: NTORS -> "6"
 Parameter: BONDS -> "5"
 Comparing "6" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET ntors 1                  ! reset chi looping variable
 Parameter: NTORS <- "1"
  
 CHARMM>     
  
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2460 ATOM PAIRS WERE FOUND FOR ATOM LIST
      240 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     14.53306      0.04830
MINI EXTERN>  *************    -27.55233      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2446 ATOM PAIRS WERE FOUND FOR ATOM LIST
      246 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2405 ATOM PAIRS WERE FOUND FOR ATOM LIST
      249 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2410 ATOM PAIRS WERE FOUND FOR ATOM LIST
      259 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2402 ATOM PAIRS WERE FOUND FOR ATOM LIST
      261 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2356 ATOM PAIRS WERE FOUND FOR ATOM LIST
      262 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2331 ATOM PAIRS WERE FOUND FOR ATOM LIST
      261 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2323 ATOM PAIRS WERE FOUND FOR ATOM LIST
      261 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2333 ATOM PAIRS WERE FOUND FOR ATOM LIST
      262 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  28585.95988*************   3247.17841      0.05547
MINI INTERN>     5049.35325    706.81083      0.00000     13.54157      0.93337
MINI EXTERN>    22813.95113      1.36972      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2322 ATOM PAIRS WERE FOUND FOR ATOM LIST
      264 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2329 ATOM PAIRS WERE FOUND FOR ATOM LIST
      266 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2316 ATOM PAIRS WERE FOUND FOR ATOM LIST
      264 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2307 ATOM PAIRS WERE FOUND FOR ATOM LIST
      268 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2271 ATOM PAIRS WERE FOUND FOR ATOM LIST
      266 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  15706.16469  12879.79519    231.63716      0.01113
MINI INTERN>     6026.67781    779.04624      0.00000     12.13269      2.20734
MINI EXTERN>     8884.28203      1.81859      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2223 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  14583.48130   1122.68339    591.84305      0.01286
MINI INTERN>     5378.64581    862.21448      0.00000     11.46478      2.18832
MINI EXTERN>     8327.23354      1.73437      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2180 ATOM PAIRS WERE FOUND FOR ATOM LIST
      272 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  13975.66510    607.81620    689.80494      0.01486
MINI INTERN>     5049.75434    926.44681      0.00000     10.65103      1.74445
MINI EXTERN>     7985.96412      1.10435      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100  13462.26504    513.40006    334.97541      0.00715
MINI INTERN>     4814.98900    930.52874      0.00000      9.83802      1.54474
MINI EXTERN>     7704.86600      0.49855      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       104
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2149 ATOM PAIRS WERE FOUND FOR ATOM LIST
      267 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120  13142.68489    319.58014    389.68197      0.00827
MINI INTERN>     4639.07098    920.41296      0.00000      9.23841      1.45413
MINI EXTERN>     7572.38994      0.11846      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140  12839.82689    302.85800    139.52255      0.00398
MINI INTERN>     4497.29221    914.34235      0.00000      8.88788      1.37849
MINI EXTERN>     7417.98092     -0.05495      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       141
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2130 ATOM PAIRS WERE FOUND FOR ATOM LIST
      259 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  12637.72173    202.10516    211.33278      0.00460
MINI INTERN>     4383.33833    913.51822      0.00000      8.78200      1.32028
MINI EXTERN>     7330.87970     -0.11680      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180  12517.58381    120.13792    249.55261      0.00531
MINI INTERN>     4304.68946    912.61410      0.00000      8.89354      1.30180
MINI EXTERN>     7290.20788     -0.12297      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  12415.63281    101.95100     60.87861      0.00256
MINI INTERN>     4259.85845    908.62060      0.00000      9.11140      1.36269
MINI EXTERN>     7236.80420     -0.12453      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200  12415.63281    101.95100     60.87861      0.00307
STPD INTERN>     4259.85845    908.62060      0.00000      9.11140      1.36269
STPD EXTERN>     7236.80420     -0.12453      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     2130 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2099 ATOM PAIRS WERE FOUND FOR ATOM LIST
      258 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0  12415.63281    101.95100     60.87861      0.00000
MINI INTERN>     4259.85845    908.62060      0.00000      9.11140      1.36269
MINI EXTERN>     7236.80420     -0.12453      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2032 ATOM PAIRS WERE FOUND FOR ATOM LIST
      262 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1995 ATOM PAIRS WERE FOUND FOR ATOM LIST
      265 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1951 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1984 ATOM PAIRS WERE FOUND FOR ATOM LIST
      267 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1965 ATOM PAIRS WERE FOUND FOR ATOM LIST
      274 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20  10975.71162   1439.92119    930.23757      0.09807
MINI INTERN>     4118.41733    565.30900      0.00000     11.84398     10.30638
MINI EXTERN>     6269.46179      0.37314      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1969 ATOM PAIRS WERE FOUND FOR ATOM LIST
      275 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        36
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1971 ATOM PAIRS WERE FOUND FOR ATOM LIST
      276 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40  10589.18851    386.52311    178.99481      0.03890
MINI INTERN>     4002.41302    542.91167      0.00000     10.64722      9.94914
MINI EXTERN>     6023.12088      0.14657      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        52
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1991 ATOM PAIRS WERE FOUND FOR ATOM LIST
      276 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2027 ATOM PAIRS WERE FOUND FOR ATOM LIST
      285 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60  10416.27747    172.91104    125.93550      0.05556
MINI INTERN>     3858.65446    560.92778      0.00000      3.99359      7.68580
MINI EXTERN>     5984.17891      0.83693      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        66
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2055 ATOM PAIRS WERE FOUND FOR ATOM LIST
      292 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        77
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2068 ATOM PAIRS WERE FOUND FOR ATOM LIST
      288 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80  10356.97075     59.30672     71.49449      0.03047
MINI INTERN>     3763.60440    541.16078      0.00000      4.52550      6.79351
MINI EXTERN>     6040.01087      0.87569      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        81
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2064 ATOM PAIRS WERE FOUND FOR ATOM LIST
      293 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        84
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2042 ATOM PAIRS WERE FOUND FOR ATOM LIST
      294 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        85
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2056 ATOM PAIRS WERE FOUND FOR ATOM LIST
      292 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        86
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2041 ATOM PAIRS WERE FOUND FOR ATOM LIST
      294 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        94
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2032 ATOM PAIRS WERE FOUND FOR ATOM LIST
      291 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       100
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      291 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100  10192.65694    164.31381     74.63574      0.03227
MINI INTERN>     3714.11233    463.43182      0.00000      6.60757      4.61150
MINI EXTERN>     6002.76730      1.12642      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120  10167.35745     25.29949     27.63659      0.01556
MINI INTERN>     3677.29827    472.90280      0.00000      2.95034      3.62587
MINI EXTERN>     6009.62674      0.95342      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       121
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2022 ATOM PAIRS WERE FOUND FOR ATOM LIST
      276 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       124
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2019 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       125
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2026 ATOM PAIRS WERE FOUND FOR ATOM LIST
      275 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       127
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2020 ATOM PAIRS WERE FOUND FOR ATOM LIST
      273 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step       138
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2013 ATOM PAIRS WERE FOUND FOR ATOM LIST
      270 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140  10077.40566     89.95180     51.54786      0.01537
MINI INTERN>     3666.36304    456.59102      0.00000      1.55213      2.24601
MINI EXTERN>     5950.36665      0.28680      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       148
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1998 ATOM PAIRS WERE FOUND FOR ATOM LIST
      274 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160  10019.97480     57.43085     69.06245      0.01649
MINI INTERN>     3635.06748    446.05777      0.00000      2.71957      1.51201
MINI EXTERN>     5934.03285      0.58512      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       164
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1991 ATOM PAIRS WERE FOUND FOR ATOM LIST
      269 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180  10004.96201     15.01279     19.88592      0.00371
MINI INTERN>     3649.38117    416.87589      0.00000      1.10449      1.45750
MINI EXTERN>     5935.66028      0.48269      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200  10002.42291      2.53910     21.64698      0.00348
MINI INTERN>     3644.92063    413.91145      0.00000      0.65733      1.34822
MINI EXTERN>     5941.24184      0.34344      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220  10001.95125      0.47166      5.27490      0.00196
MINI INTERN>     3644.30262    413.03522      0.00000      0.70773      1.30403
MINI EXTERN>     5942.28650      0.31515      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240  10001.79728      0.15396      0.84053      0.00040
MINI INTERN>     3646.97604    410.32970      0.00000      0.72895      1.26989
MINI EXTERN>     5942.21684      0.27585      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260  10001.78652      0.01077      0.21517      0.00022
MINI INTERN>     3647.08150    410.10198      0.00000      0.72336      1.26802
MINI EXTERN>     5942.33776      0.27390      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       263
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1984 ATOM PAIRS WERE FOUND FOR ATOM LIST
      267 GROUP PAIRS REQUIRED ATOM SEARCHES


 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      278  10001.78336      0.00316      0.08551      0.00005
ABNR INTERN>     3647.56560    409.96556      0.00000      0.72090      1.26439
ABNR EXTERN>     5941.99579      0.27112      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    STREAM UNIT 35

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "9"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "9" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "9"
 Comparing "9" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "9"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "9" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "9"
 Comparing "9" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "9"
 VOPEN> Attempting to open::frames/frame9.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame9.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * 10001.8 3647.57 409.966 0.720895 5942 0.271122
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "10001.8"
 Parameter: ELAST <- "10001.8"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>     
  
 CHARMM>    LABEL mcloop
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.746419"
 Parameter: CHICHOICE1 <- "0.746419"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.746419"
 Parameter: BONDS -> "5"
Evaluating: INT(0.746419*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 6.72846E-02
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.852271"
 Parameter: CHI <- "0.852271"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.852271"
Evaluating: (0.852271*360)-180.0
 Parameter: CHI3 <- "126.818"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "126.818"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1804 ATOM PAIRS WERE FOUND FOR ATOM LIST
      163 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     11.62269      0.04830
MINI EXTERN>  *************      5.63154      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1791 ATOM PAIRS WERE FOUND FOR ATOM LIST
      161 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1772 ATOM PAIRS WERE FOUND FOR ATOM LIST
      165 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1720 ATOM PAIRS WERE FOUND FOR ATOM LIST
      168 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1721 ATOM PAIRS WERE FOUND FOR ATOM LIST
      173 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1706 ATOM PAIRS WERE FOUND FOR ATOM LIST
      172 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   5932.34753*************    771.96171      0.02311
MINI INTERN>     1212.90216    138.25897      0.00000     12.78915      1.97332
MINI EXTERN>     4569.23879     -2.81487      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1670 ATOM PAIRS WERE FOUND FOR ATOM LIST
      167 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        40
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1655 ATOM PAIRS WERE FOUND FOR ATOM LIST
      162 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   3464.67559   2467.67194    457.93818      0.02670
MINI INTERN>      885.31382    152.98994      0.00000     13.64028      2.97983
MINI EXTERN>     2411.13300     -1.38128      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1617 ATOM PAIRS WERE FOUND FOR ATOM LIST
      152 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1578 ATOM PAIRS WERE FOUND FOR ATOM LIST
      147 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   1309.63021   2155.04538    207.88098      0.03086
MINI INTERN>      249.04342    242.17397      0.00000     13.91947      9.86638
MINI EXTERN>      797.32379     -2.69682      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        70
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1525 ATOM PAIRS WERE FOUND FOR ATOM LIST
      134 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80    436.97811    872.65210     44.23332      0.03566
MINI INTERN>       33.77496    161.10421      0.00000     11.43989      6.73670
MINI EXTERN>      227.63520     -3.71285      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        81
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1462 ATOM PAIRS WERE FOUND FOR ATOM LIST
      134 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        87
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1423 ATOM PAIRS WERE FOUND FOR ATOM LIST
      133 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        93
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1410 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     90.90977    346.06834     18.44506      0.01717
MINI INTERN>        7.52831     27.35316      0.00000     10.38031      3.54947
MINI EXTERN>       43.43411     -1.33558      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       108
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1375 ATOM PAIRS WERE FOUND FOR ATOM LIST
      124 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     49.78367     41.12611      5.45061      0.00827
MINI INTERN>        2.35572     19.32055      0.00000      9.50233      1.65673
MINI EXTERN>       18.28820     -1.33986      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     32.53496     17.24871     13.05844      0.00955
MINI INTERN>        2.33313     15.29876      0.00000      8.10835      0.84385
MINI EXTERN>        7.41282     -1.46195      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       148
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1318 ATOM PAIRS WERE FOUND FOR ATOM LIST
      126 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     21.08459     11.45037      4.35116      0.00460
MINI INTERN>        0.88871     11.68890      0.00000      6.98785      0.50329
MINI EXTERN>        2.56723     -1.55139      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     14.57765      6.50694      6.72305      0.00531
MINI INTERN>        0.90308      9.31256      0.00000      6.06430      0.29684
MINI EXTERN>       -0.36721     -1.63192      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      9.72336      4.85429      2.18735      0.00256
MINI INTERN>        0.43808      7.66880      0.00000      5.33704      0.17723
MINI EXTERN>       -2.20003     -1.69775      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      9.72336      4.85429      2.18735      0.00307
STPD INTERN>        0.43808      7.66880      0.00000      5.33704      0.17723
STPD EXTERN>       -2.20003     -1.69775      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1318 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1311 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      9.72336      4.85429      2.18735      0.00000
MINI INTERN>        0.43808      7.66880      0.00000      5.33704      0.17723
MINI EXTERN>       -2.20003     -1.69775      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1281 ATOM PAIRS WERE FOUND FOR ATOM LIST
      134 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1262 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1231 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -9.19038     18.91374      3.24020      0.01668
MINI INTERN>        0.22598      1.86825      0.00000      0.68694      0.03182
MINI EXTERN>      -10.39117     -1.61221      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       40     -9.96529      0.77491      0.48015      0.00338
MINI INTERN>        0.14124      1.77325      0.00000      0.74384      0.00514
MINI EXTERN>      -10.86213     -1.76663      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1226 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60    -10.48593      0.52064      0.97206      0.00528
MINI INTERN>        0.21806      1.73622      0.00000      0.79706      0.00815
MINI EXTERN>      -11.39835     -1.84707      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        78
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1235 ATOM PAIRS WERE FOUND FOR ATOM LIST
      133 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80    -11.17348      0.68755      0.50036      0.00496
MINI INTERN>        0.13398      1.74444      0.00000      0.94134      0.00452
MINI EXTERN>      -11.83131     -2.16645      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100    -11.65353      0.48005      0.91288      0.00465
MINI INTERN>        0.18266      1.73235      0.00000      1.00541      0.00952
MINI EXTERN>      -11.82244     -2.76104      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120    -11.81688      0.16335      0.48396      0.00262
MINI INTERN>        0.14851      1.67547      0.00000      1.00593      0.01541
MINI EXTERN>      -11.88909     -2.77312      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140    -11.99889      0.18201      0.70138      0.00409
MINI INTERN>        0.15909      1.69237      0.00000      1.07308      0.05634
MINI EXTERN>      -12.11104     -2.86873      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160    -12.04865      0.04976      0.27568      0.00138
MINI INTERN>        0.15740      1.66971      0.00000      1.08207      0.03440
MINI EXTERN>      -12.13302     -2.85922      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       170
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1219 ATOM PAIRS WERE FOUND FOR ATOM LIST
      136 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180    -12.18400      0.13535      0.33187      0.00216
MINI INTERN>        0.14320      1.70446      0.00000      1.23106      0.04635
MINI EXTERN>      -12.55716     -2.75190      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200    -12.21400      0.03000      0.22112      0.00122
MINI INTERN>        0.15126      1.67341      0.00000      1.23369      0.04963
MINI EXTERN>      -12.48896     -2.83303      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      213    -12.21798      0.00398      0.08808      0.00046
ABNR INTERN>        0.15705      1.70299      0.00000      1.24148      0.05394
ABNR EXTERN>      -12.50277     -2.87067      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "10001.8"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.218"
 Comparing "-12.218" and "10001.8".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "10001.8"
 RDCMND substituted energy or value "?ENER" to "-12.218"
 Comparing "-12.218" and "10001.8".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1075.9712  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.766703
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.7667"
 Parameter: RMSD <- "8.7667"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.7667"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.7667" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.7667"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.7667" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.7667"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.7667" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "9"
 Comparing "2" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1273.3746  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.537050
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.53705"
 Parameter: RMSD <- "9.53705"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.53705"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.53705" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.53705"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.53705" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.53705"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.53705" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "9"
 Comparing "3" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1298.6475  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.631227
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.63123"
 Parameter: RMSD <- "9.63123"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.63123"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.63123" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.63123"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.63123" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.63123"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.63123" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "9"
 Comparing "4" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1817.9418  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   11.395306
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "11.3953"
 Parameter: RMSD <- "11.3953"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "11.3953"
 Parameter: RMSTOL -> "0.05"
 Comparing "11.3953" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "11.3953"
 Parameter: RMSTOL -> "0.05"
 Comparing "11.3953" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "11.3953"
 Parameter: RMSTOL -> "0.05"
 Comparing "11.3953" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "9"
 Comparing "5" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1580.0469  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.623582
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.6236"
 Parameter: RMSD <- "10.6236"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.6236"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.6236" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.6236"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.6236" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.6236"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.6236" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "9"
 Comparing "6" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "6"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame6.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1387.3676  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.954782
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.95478"
 Parameter: RMSD <- "9.95478"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.95478"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.95478" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.95478"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.95478" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.95478"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.95478" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "7"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "7"
 Parameter: ACCEPTS -> "9"
 Comparing "7" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "7"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame7.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame7.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    155.8961  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.336980
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.33698"
 Parameter: RMSD <- "3.33698"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.33698"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.33698" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.33698"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.33698" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.33698"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.33698" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "8"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "8"
 Parameter: ACCEPTS -> "9"
 Comparing "8" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "8"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame8.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame8.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS     91.8916  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    2.561969
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "2.56197"
 Parameter: RMSD <- "2.56197"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "2.56197"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.56197" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "2.56197"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.56197" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "2.56197"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.56197" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "9"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "9"
 Parameter: ACCEPTS -> "9"
 Comparing "9" and "9".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "9"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame9.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame9.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:34      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    568.1380  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    6.370344
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "6.37034"
 Parameter: RMSD <- "6.37034"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "6.37034"
 Parameter: RMSTOL -> "0.05"
 Comparing "6.37034" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "6.37034"
 Parameter: RMSTOL -> "0.05"
 Comparing "6.37034" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "6.37034"
 Parameter: RMSTOL -> "0.05"
 Comparing "6.37034" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "10"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "10"
 Parameter: ACCEPTS -> "9"
 Comparing "10" and "9".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "10001.8"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.218"
 Comparing "-12.218" and "10001.8".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "10001.8"
 RDCMND substituted energy or value "?ENER" to "-12.218"
 Comparing "-12.218" and "10001.8".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "6.37034"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6.37034" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "6.37034"
 Parameter: RMSTOL -> "0.05"
 Comparing "6.37034" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "10"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "10"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "10" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "10"
 Comparing "10" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "10"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "10" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "10"
 Comparing "10" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "10"
 VOPEN> Attempting to open::frames/frame10.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame10.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -12.218 0.157055 1.70299 1.24148 -12.5028 -2.87067
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-12.218"
 Parameter: ELAST <- "-12.218"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "1"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "0"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.113224"
 Parameter: CHICHOICE1 <- "0.113224"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.113224"
 Parameter: BONDS -> "5"
Evaluating: INT(0.113224*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.954481
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.961659"
 Parameter: CHI <- "0.961659"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.961659"
Evaluating: (0.961659*360)-180.0
 Parameter: CHI5 <- "166.197"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "166.197"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1688 ATOM PAIRS WERE FOUND FOR ATOM LIST
      153 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     11.62269      0.04830
MINI EXTERN>  *************    -28.51275      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1679 ATOM PAIRS WERE FOUND FOR ATOM LIST
      153 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1665 ATOM PAIRS WERE FOUND FOR ATOM LIST
      161 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1642 ATOM PAIRS WERE FOUND FOR ATOM LIST
      175 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1637 ATOM PAIRS WERE FOUND FOR ATOM LIST
      175 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1594 ATOM PAIRS WERE FOUND FOR ATOM LIST
      176 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1595 ATOM PAIRS WERE FOUND FOR ATOM LIST
      194 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1584 ATOM PAIRS WERE FOUND FOR ATOM LIST
      186 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1567 ATOM PAIRS WERE FOUND FOR ATOM LIST
      179 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   3239.49174*************     85.00815      0.05547
MINI INTERN>     2217.10248    116.81864      0.00000     15.14490      1.02843
MINI EXTERN>      894.39797     -5.00068      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1550 ATOM PAIRS WERE FOUND FOR ATOM LIST
      185 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        34
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1515 ATOM PAIRS WERE FOUND FOR ATOM LIST
      177 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   2411.61303    827.87871     75.84902      0.02670
MINI INTERN>     1830.73845     94.72600      0.00000     16.23872      0.11304
MINI EXTERN>      476.31246     -6.51563      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1512 ATOM PAIRS WERE FOUND FOR ATOM LIST
      174 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1504 ATOM PAIRS WERE FOUND FOR ATOM LIST
      170 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1485 ATOM PAIRS WERE FOUND FOR ATOM LIST
      168 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        50
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1485 ATOM PAIRS WERE FOUND FOR ATOM LIST
      168 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        52
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1476 ATOM PAIRS WERE FOUND FOR ATOM LIST
      166 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1459 ATOM PAIRS WERE FOUND FOR ATOM LIST
      163 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        54
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1458 ATOM PAIRS WERE FOUND FOR ATOM LIST
      161 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        55
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1441 ATOM PAIRS WERE FOUND FOR ATOM LIST
      160 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1429 ATOM PAIRS WERE FOUND FOR ATOM LIST
      154 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1415 ATOM PAIRS WERE FOUND FOR ATOM LIST
      152 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60    244.29321   2167.31983     64.45093      0.07406
MINI INTERN>       49.33273    114.77319      0.00000     17.69664      0.34926
MINI EXTERN>       67.73008     -5.58870      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        63
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1387 ATOM PAIRS WERE FOUND FOR ATOM LIST
      143 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        73
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1366 ATOM PAIRS WERE FOUND FOR ATOM LIST
      137 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     61.22468    183.06852     19.02233      0.01486
MINI INTERN>        7.79826     27.81415      0.00000     18.29740      2.60070
MINI EXTERN>        9.69469     -4.98052      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        92
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1339 ATOM PAIRS WERE FOUND FOR ATOM LIST
      138 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     37.97476     23.24992      5.88669      0.00715
MINI INTERN>        2.32606     17.58035      0.00000     17.91526      3.83135
MINI EXTERN>        1.10464     -4.78290      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     30.97524      6.99953      2.49937      0.00344
MINI INTERN>        1.80294     15.02626      0.00000     17.57785      4.14080
MINI EXTERN>       -2.88321     -4.68940      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     26.92068      4.05456      5.19545      0.00398
MINI INTERN>        1.89334     13.61928      0.00000     17.04075      4.33831
MINI EXTERN>       -5.41635     -4.55466      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     24.11753      2.80315      5.86062      0.00460
MINI INTERN>        1.84956     12.78679      0.00000     16.22597      4.54485
MINI EXTERN>       -6.88847     -4.40118      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       162
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1293 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     21.50067      2.61686      2.08797      0.00221
MINI INTERN>        1.24847     12.31332      0.00000     15.14231      4.84364
MINI EXTERN>       -7.82900     -4.21808      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     19.52358      1.97708      1.97974      0.00256
MINI INTERN>        1.15651     11.84415      0.00000     13.99564      5.09977
MINI EXTERN>       -8.52365     -4.04883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     19.52358      1.97708      1.97974      0.00307
STPD INTERN>        1.15651     11.84415      0.00000     13.99564      5.09977
STPD EXTERN>       -8.52365     -4.04883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1293 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1287 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     19.52358      1.97708      1.97974      0.00000
MINI INTERN>        1.15651     11.84415      0.00000     13.99564      5.09977
MINI EXTERN>       -8.52365     -4.04883      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1268 ATOM PAIRS WERE FOUND FOR ATOM LIST
      129 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20      9.80908      9.71451      6.20766      0.03013
MINI INTERN>        0.74730      9.40103      0.00000      8.85717      4.72140
MINI EXTERN>      -12.24492     -1.67290      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1231 ATOM PAIRS WERE FOUND FOR ATOM LIST
      126 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1212 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        27
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1166 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        35
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1135 ATOM PAIRS WERE FOUND FOR ATOM LIST
      120 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        40
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1107 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -3.75495     13.56402      5.52289      0.03101
MINI INTERN>        0.67123      3.82814      0.00000      5.84585      0.93270
MINI EXTERN>      -13.94332     -1.08953      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1089 ATOM PAIRS WERE FOUND FOR ATOM LIST
      113 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -7.36680      3.61186      1.75289      0.01164
MINI INTERN>        0.21445      2.18549      0.00000      4.04023      0.75572
MINI EXTERN>      -13.48893     -1.07377      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -9.04092      1.67412      2.04086      0.01092
MINI INTERN>        0.15933      1.34354      0.00000      3.88691      0.37316
MINI EXTERN>      -13.79453     -1.00933      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        83
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1131 ATOM PAIRS WERE FOUND FOR ATOM LIST
      115 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100    -10.19282      1.15190      1.23015      0.00614
MINI INTERN>        0.08301      0.92898      0.00000      3.96229      0.12675
MINI EXTERN>      -14.37602     -0.91783      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120    -10.48308      0.29026      0.52200      0.00346
MINI INTERN>        0.08348      0.91611      0.00000      3.96945      0.07615
MINI EXTERN>      -14.73990     -0.78837      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       123
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1184 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140    -10.76989      0.28681      0.34133      0.00195
MINI INTERN>        0.07463      0.99665      0.00000      3.87571      0.12030
MINI EXTERN>      -15.04015     -0.79703      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160    -10.86232      0.09243      0.56632      0.00304
MINI INTERN>        0.05702      1.04394      0.00000      3.86224      0.12781
MINI EXTERN>      -15.19469     -0.75864      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180    -11.01785      0.15553      0.49891      0.00286
MINI INTERN>        0.07297      1.08169      0.00000      3.92498      0.11433
MINI EXTERN>      -15.43373     -0.77809      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       188
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1200 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200    -11.22303      0.20518      0.48328      0.00268
MINI INTERN>        0.09194      1.22176      0.00000      4.08724      0.10577
MINI EXTERN>      -15.95950     -0.77024      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220    -11.26578      0.04275      0.31410      0.00151
MINI INTERN>        0.08612      1.23957      0.00000      4.08700      0.09191
MINI EXTERN>      -16.00762     -0.76275      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      229    -11.27012      0.00435      0.08908      0.00053
ABNR INTERN>        0.08140      1.24479      0.00000      4.09629      0.09722
ABNR EXTERN>      -16.02616     -0.76367      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.218"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-11.2701"
 Comparing "-11.2701" and "-12.218".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.218"
 RDCMND substituted energy or value "?ENER" to "-11.2701"
 Comparing "-11.2701" and "-12.218".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.218"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-11.2701"
 Comparing "-11.2701" and "-12.218".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.218"
 RDCMND substituted energy or value "?ENER" to "-11.2701"
 Comparing "-11.2701" and "-12.218".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.607622"
 Parameter: R <- "0.607622"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-12.218"
 RDCMND substituted energy or value "?ENER" to "-11.2701"
Evaluating: -11.2701--12.218
 Parameter: DELE <- "0.947901"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "0.947901"
Evaluating: 1.00654*0.947901
 Parameter: BETADELE <- "0.9541"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "0.9541"
Evaluating: EXP(-0.9541)
 Parameter: DELN <- "0.385159"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.385159"
 Parameter: R -> "0.607622"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.385159" and "0.607622".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.385159"
 Parameter: R -> "0.607622"
 Comparing "0.385159" and "0.607622".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "1"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "2"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "1"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "1" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.309328"
 Parameter: CHICHOICE1 <- "0.309328"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.309328"
 Parameter: BONDS -> "5"
Evaluating: INT(0.309328*5)
 Parameter: CHICHOICE2 <- "1"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "1"
 Parameter: BONDS -> "5"
 Comparing "1" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "1"
 Parameter: CHICHOICE2 -> "1"
 Comparing "1" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str::
 OPNLGU> Unit 21 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi1.str
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    21
 RDTITL> SET CHI 0.877852
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "5.354349E-02"
 Parameter: CHI <- "5.354349E-02"
  
 CHARMM>    CALC chi1 = (@chi*360) - 180.0
 Parameter: CHI -> "5.354349E-02"
Evaluating: (5.354349E-02*360)-180.0
 Parameter: CHI1 <- "-160.724"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 @chi1
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1 -> "-160.724"
               FOUND IN IC  564 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    !Write coordinates to a disk file
 CHARMM>    OPEN WRITE UNIT 41 CARD NAME "temp.pdb"
 VOPEN> Attempting to open::temp.pdb::
 OPNLGU> Unit 41 opened for WRITE access to temp.pdb
  
 CHARMM>    WRITE COOR PDB UNIT 41 CARD
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
  * WARNING * <PARSUB> Command ignored. Token not found: >PROTEIN<

      ***** LEVEL  0 WARNING FROM <PARSE1> *****
      ***** Error in parameter substitution.
      ******************************************
      BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5

 RDTITL> 
 RDTITL> *POLAR HYDROGEN POSITIONS GENERATED USING HBUILD
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 41
 VCLOSE: Closing unit   41 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   21 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI1COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "1"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "1" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1461 ATOM PAIRS WERE FOUND FOR ATOM LIST
      146 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      6.39984      0.04830
MINI EXTERN>  *************    352.90900      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1465 ATOM PAIRS WERE FOUND FOR ATOM LIST
      144 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1459 ATOM PAIRS WERE FOUND FOR ATOM LIST
      142 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1446 ATOM PAIRS WERE FOUND FOR ATOM LIST
      138 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1426 ATOM PAIRS WERE FOUND FOR ATOM LIST
      137 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1394 ATOM PAIRS WERE FOUND FOR ATOM LIST
      144 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1369 ATOM PAIRS WERE FOUND FOR ATOM LIST
      141 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    393.41723*************     44.62092      0.05547
MINI INTERN>       65.73299    129.79057      0.00000      6.65731      1.79693
MINI EXTERN>      190.14214     -0.70271      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1346 ATOM PAIRS WERE FOUND FOR ATOM LIST
      140 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1320 ATOM PAIRS WERE FOUND FOR ATOM LIST
      139 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     98.94850    294.46873     37.68672      0.02670
MINI INTERN>       12.32927     37.01259      0.00000      9.63424      0.41012
MINI EXTERN>       40.91050     -1.34823      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        50
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1292 ATOM PAIRS WERE FOUND FOR ATOM LIST
      139 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     44.60519     54.34331     20.05925      0.01286
MINI INTERN>        4.35180     15.67556      0.00000     11.65948      0.41649
MINI EXTERN>       14.20958     -1.70772      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     23.87137     20.73383      4.33945      0.00619
MINI INTERN>        0.64146      9.12806      0.00000     11.56161      0.21600
MINI EXTERN>        4.07064     -1.74641      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        86
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1247 ATOM PAIRS WERE FOUND FOR ATOM LIST
      137 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     12.88336     10.98800      9.91005      0.00715
MINI INTERN>        0.68867      6.22705      0.00000     10.10698      0.06599
MINI EXTERN>       -2.49467     -1.71066      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120      6.20219      6.68118     10.66979      0.00827
MINI INTERN>        0.74703      4.80775      0.00000      8.61332      0.02300
MINI EXTERN>       -6.32656     -1.66235      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       128
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1220 ATOM PAIRS WERE FOUND FOR ATOM LIST
      137 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140      0.97721      5.22497      2.94359      0.00398
MINI INTERN>        0.21425      3.41111      0.00000      7.59565      0.06425
MINI EXTERN>       -8.68519     -1.62286      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -1.68296      2.66018      1.68995      0.00192
MINI INTERN>        0.08788      2.93757      0.00000      6.94447      0.12483
MINI EXTERN>      -10.18211     -1.59561      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -3.39241      1.70945      2.68908      0.00221
MINI INTERN>        0.09395      2.63746      0.00000      6.45794      0.18874
MINI EXTERN>      -11.19718     -1.57332      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -4.51760      1.12519      3.59015      0.00256
MINI INTERN>        0.13435      2.46975      0.00000      6.08301      0.24803
MINI EXTERN>      -11.89842     -1.55431      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     -4.51760      1.12519      3.59015      0.00128
STPD INTERN>        0.13435      2.46975      0.00000      6.08301      0.24803
STPD EXTERN>      -11.89842     -1.55431      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1220 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1197 ATOM PAIRS WERE FOUND FOR ATOM LIST
      133 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     -4.53925      0.02165      1.81061      0.00000
MINI INTERN>        0.12829      2.38329      0.00000      6.12052      0.24245
MINI EXTERN>      -11.86011     -1.55370      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1161 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -8.52051      3.98126      1.19954      0.00667
MINI INTERN>        0.17212      2.50730      0.00000      3.98770      0.80561
MINI EXTERN>      -14.64565     -1.34759      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1178 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1190 ATOM PAIRS WERE FOUND FOR ATOM LIST
      126 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40    -11.59908      3.07857      1.33721      0.00626
MINI INTERN>        0.07442      1.78835      0.00000      2.36716      0.21333
MINI EXTERN>      -15.28377     -0.75858      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60    -12.13457      0.53549      0.69859      0.00352
MINI INTERN>        0.10192      1.64889      0.00000      1.92822      0.19521
MINI EXTERN>      -15.20984     -0.79898      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80    -12.40288      0.26831      0.63117      0.00330
MINI INTERN>        0.10343      1.59111      0.00000      1.72623      0.16976
MINI EXTERN>      -15.07912     -0.91429      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100    -12.48501      0.08214      0.28212      0.00186
MINI INTERN>        0.09732      1.55244      0.00000      1.72548      0.13086
MINI EXTERN>      -15.07799     -0.91312      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       116
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1200 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120    -12.59046      0.10544      0.43363      0.00291
MINI INTERN>        0.08662      1.52223      0.00000      1.63714      0.12918
MINI EXTERN>      -15.07032     -0.89530      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140    -12.69509      0.10463      0.58948      0.00273
MINI INTERN>        0.09372      1.36093      0.00000      1.51094      0.08325
MINI EXTERN>      -14.93025     -0.81366      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160    -12.75744      0.06236      0.25680      0.00154
MINI INTERN>        0.09707      1.45886      0.00000      1.48415      0.10028
MINI EXTERN>      -15.09331     -0.80448      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180    -12.79483      0.03739      0.30791      0.00144
MINI INTERN>        0.09779      1.49497      0.00000      1.46033      0.11375
MINI EXTERN>      -15.18618     -0.77549      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200    -12.81462      0.01979      0.28942      0.00135
MINI INTERN>        0.08977      1.48301      0.00000      1.43595      0.09813
MINI EXTERN>      -15.14764     -0.77383      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       220
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1201 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      220    -12.84104      0.02643      0.12460      0.00076
MINI INTERN>        0.08081      1.44064      0.00000      1.39163      0.09079
MINI EXTERN>      -15.06688     -0.77804      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240    -12.86265      0.02161      0.23476      0.00119
MINI INTERN>        0.08694      1.44429      0.00000      1.35417      0.08860
MINI EXTERN>      -15.06543     -0.77123      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      247    -12.86555      0.00289      0.07995      0.00051
ABNR INTERN>        0.08614      1.45468      0.00000      1.35926      0.08995
ABNR EXTERN>      -15.08510     -0.77047      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.218"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.8655"
 Comparing "-12.8655" and "-12.218".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.218"
 RDCMND substituted energy or value "?ENER" to "-12.8655"
 Comparing "-12.8655" and "-12.218".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1400.7323  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.002615
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.0026"
 Parameter: RMSD <- "10.0026"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.0026"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0026" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.0026"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0026" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.0026"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0026" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "10"
 Comparing "2" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1438.6043  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.136935
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.1369"
 Parameter: RMSD <- "10.1369"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.1369"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1369" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.1369"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1369" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.1369"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1369" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "10"
 Comparing "3" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    964.2327  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.299022
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.29902"
 Parameter: RMSD <- "8.29902"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.29902"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.29902" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.29902"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.29902" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.29902"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.29902" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "10"
 Comparing "4" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1529.8762  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.453558
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.4536"
 Parameter: RMSD <- "10.4536"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.4536"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.4536" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.4536"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.4536" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.4536"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.4536" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "10"
 Comparing "5" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1241.3122  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.416218
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.41622"
 Parameter: RMSD <- "9.41622"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.41622"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.41622" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.41622"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.41622" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.41622"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.41622" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "10"
 Comparing "6" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "6"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame6.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1356.0341  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.841726
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.84173"
 Parameter: RMSD <- "9.84173"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.84173"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84173" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.84173"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84173" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.84173"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84173" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "7"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "7"
 Parameter: ACCEPTS -> "10"
 Comparing "7" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "7"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame7.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame7.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    171.0060  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.494956
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.49496"
 Parameter: RMSD <- "3.49496"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.49496"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.49496" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.49496"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.49496" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.49496"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.49496" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "8"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "8"
 Parameter: ACCEPTS -> "10"
 Comparing "8" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "8"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame8.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame8.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    186.7142  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.651948
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.65195"
 Parameter: RMSD <- "3.65195"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.65195"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.65195" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.65195"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.65195" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.65195"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.65195" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "9"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "9"
 Parameter: ACCEPTS -> "10"
 Comparing "9" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "9"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame9.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame9.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:34      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    362.2240  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    5.086565
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "5.08656"
 Parameter: RMSD <- "5.08656"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "5.08656"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.08656" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "5.08656"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.08656" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "5.08656"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.08656" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "10"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "10"
 Parameter: ACCEPTS -> "10"
 Comparing "10" and "10".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "10"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame10.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame10.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:34      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    135.7107  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.113458
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.11346"
 Parameter: RMSD <- "3.11346"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.11346"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.11346" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.11346"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.11346" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.11346"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.11346" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "11"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "11"
 Parameter: ACCEPTS -> "10"
 Comparing "11" and "10".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.218"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.8655"
 Comparing "-12.8655" and "-12.218".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.218"
 RDCMND substituted energy or value "?ENER" to "-12.8655"
 Comparing "-12.8655" and "-12.218".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "3.11346"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "3.11346" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "3.11346"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.11346" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "11"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "11"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "11" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "11"
 Comparing "11" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "11"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "11" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "11"
 Comparing "11" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "11"
 VOPEN> Attempting to open::frames/frame11.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame11.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -12.8655 8.613565E-02 1.45468 1.35926 -15.0851 -0.770473
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-12.8655"
 Parameter: ELAST <- "-12.8655"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "3"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "1"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "1" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.905466"
 Parameter: CHICHOICE1 <- "0.905466"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.905466"
 Parameter: BONDS -> "5"
Evaluating: INT(0.905466*5)
 Parameter: CHICHOICE2 <- "4"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "4"
 Parameter: BONDS -> "5"
 Comparing "4" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "4"
 Parameter: CHICHOICE2 -> "4"
 Comparing "4" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "4"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str::
 OPNLGU> Unit 24 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi4.str
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    24
 RDTITL> SET CHI 0.172776
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.844866"
 Parameter: CHI <- "0.844866"
  
 CHARMM>    CALC chi4 = (@chi*360) - 180.0
 Parameter: CHI -> "0.844866"
Evaluating: (0.844866*360)-180.0
 Parameter: CHI4 <- "124.152"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 @chi4
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4 -> "124.152"
               FOUND IN IC  567 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   24 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "4".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI4COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "4"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "4" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1189 ATOM PAIRS WERE FOUND FOR ATOM LIST
      121 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      7.09001      0.04830
MINI EXTERN>  *************    348.75600      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1193 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1187 ATOM PAIRS WERE FOUND FOR ATOM LIST
      118 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1179 ATOM PAIRS WERE FOUND FOR ATOM LIST
      117 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        13
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1159 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1142 ATOM PAIRS WERE FOUND FOR ATOM LIST
      130 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1121 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1115 ATOM PAIRS WERE FOUND FOR ATOM LIST
      127 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1110 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20    845.26526*************    214.69885      0.13312
MINI INTERN>      495.45413    120.53143      0.00000      8.57924      0.84344
MINI EXTERN>      220.88029     -1.02326      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1072 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1066 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1039 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40    113.65228    731.61298     38.09858      0.02670
MINI INTERN>       22.48062     44.80722      0.00000      7.02339      0.67564
MINI EXTERN>       39.88789     -1.22247      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        44
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1008 ATOM PAIRS WERE FOUND FOR ATOM LIST
      112 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     58.71068     54.94161     20.15213      0.01286
MINI INTERN>        6.31567     28.08823      0.00000      7.63971      0.28495
MINI EXTERN>       17.64359     -1.26147      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        68
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      987 ATOM PAIRS WERE FOUND FOR ATOM LIST
      109 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     41.46063     17.25005      8.58795      0.00619
MINI INTERN>        3.52467     21.52775      0.00000      8.80651      0.31365
MINI EXTERN>        8.52024     -1.23218      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     33.77119      7.68944      2.79346      0.00298
MINI INTERN>        2.34586     17.66096      0.00000     10.73878      0.27936
MINI EXTERN>        3.93859     -1.19234      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     28.05279      5.71840      3.55438      0.00344
MINI INTERN>        1.99515     13.31890      0.00000     12.73143      0.23408
MINI EXTERN>        0.92184     -1.14861      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       127
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      971 ATOM PAIRS WERE FOUND FOR ATOM LIST
      108 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     23.82176      4.23103      2.95347      0.00398
MINI INTERN>        1.59400     10.52231      0.00000     13.65656      0.27694
MINI EXTERN>       -1.11065     -1.11740      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     20.98206      2.83970      1.72804      0.00192
MINI INTERN>        1.27784      8.84116      0.00000     14.10520      0.36432
MINI EXTERN>       -2.51497     -1.09148      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     19.05119      1.93087      1.43971      0.00221
MINI INTERN>        1.10331      7.65035      0.00000     14.38407      0.44588
MINI EXTERN>       -3.46264     -1.06978      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     17.54966      1.50153      3.34126      0.00256
MINI INTERN>        1.04049      6.63672      0.00000     14.56965      0.53607
MINI EXTERN>       -4.19248     -1.04079      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     17.54966      1.50153      3.34126      0.00307
STPD INTERN>        1.04049      6.63672      0.00000     14.56965      0.53607
STPD EXTERN>       -4.19248     -1.04079      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are      971 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      962 ATOM PAIRS WERE FOUND FOR ATOM LIST
      105 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     17.54966      1.50153      3.34126      0.00000
MINI INTERN>        1.04049      6.63672      0.00000     14.56965      0.53607
MINI EXTERN>       -4.19248     -1.04079      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      947 ATOM PAIRS WERE FOUND FOR ATOM LIST
      108 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        17
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      933 ATOM PAIRS WERE FOUND FOR ATOM LIST
      108 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20      9.29648      8.25319      2.91631      0.01647
MINI INTERN>        0.27868      2.97365      0.00000     14.45561      1.59802
MINI EXTERN>       -9.21376     -0.79573      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      938 ATOM PAIRS WERE FOUND FOR ATOM LIST
      109 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      948 ATOM PAIRS WERE FOUND FOR ATOM LIST
      111 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      3.30003      5.99645      2.87128      0.01908
MINI INTERN>        1.13959      4.52741      0.00000      7.58873      0.10956
MINI EXTERN>       -9.47909     -0.58617      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        49
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      965 ATOM PAIRS WERE FOUND FOR ATOM LIST
      114 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        55
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1000 ATOM PAIRS WERE FOUND FOR ATOM LIST
      107 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -4.05063      7.35066      3.63544      0.02618
MINI INTERN>        0.42096      1.50166      0.00000      3.84595      0.01284
MINI EXTERN>       -8.84132     -0.99072      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        62
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1026 ATOM PAIRS WERE FOUND FOR ATOM LIST
      113 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -6.06980      2.01917      1.00184      0.00531
MINI INTERN>        0.15851      1.44829      0.00000      3.03336      0.00154
MINI EXTERN>       -9.65248     -1.05902      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        98
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1038 ATOM PAIRS WERE FOUND FOR ATOM LIST
      115 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -7.01561      0.94581      1.58720      0.00830
MINI INTERN>        0.19502      1.25028      0.00000      2.51467      0.04741
MINI EXTERN>       -9.87296     -1.15003      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -7.39702      0.38140      0.41591      0.00280
MINI INTERN>        0.15071      1.55747      0.00000      2.19324      0.10920
MINI EXTERN>      -10.30720     -1.10043      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -7.54384      0.14682      0.95604      0.00438
MINI INTERN>        0.14834      1.41244      0.00000      2.12772      0.08270
MINI EXTERN>      -10.27406     -1.04097      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -7.62719      0.08335      0.38406      0.00247
MINI INTERN>        0.13957      1.57679      0.00000      2.02064      0.05315
MINI EXTERN>      -10.46707     -0.95028      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       165
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1081 ATOM PAIRS WERE FOUND FOR ATOM LIST
      117 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      180     -7.76340      0.13621      0.87500      0.00385
MINI INTERN>        0.15636      1.60077      0.00000      1.79298      0.07977
MINI EXTERN>      -10.46145     -0.93183      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -7.84204      0.07864      0.45078      0.00217
MINI INTERN>        0.12814      1.81471      0.00000      1.87035      0.05836
MINI EXTERN>      -10.73784     -0.97577      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220     -7.91005      0.06801      0.25727      0.00122
MINI INTERN>        0.11633      1.75137      0.00000      1.89333      0.07686
MINI EXTERN>      -10.70209     -1.04585      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      240     -7.92437      0.01432      0.14577      0.00069
MINI INTERN>        0.12068      1.71222      0.00000      1.85713      0.07588
MINI EXTERN>      -10.66291     -1.02737      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      242     -7.92523      0.00086      0.08047      0.00050
ABNR INTERN>        0.12296      1.71343      0.00000      1.85548      0.07498
ABNR EXTERN>      -10.66616     -1.02591      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-7.92523"
 Comparing "-7.92523" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-7.92523"
 Comparing "-7.92523" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-7.92523"
 Comparing "-7.92523" and "-12.8655".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-7.92523"
 Comparing "-7.92523" and "-12.8655".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.655506"
 Parameter: R <- "0.655506"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-7.92523"
Evaluating: -7.92523--12.8655
 Parameter: DELE <- "4.94027"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "4.94027"
Evaluating: 1.00654*4.94027
 Parameter: BETADELE <- "4.97258"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "4.97258"
Evaluating: EXP(-4.97258)
 Parameter: DELN <- "6.925258E-03"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "6.925258E-03"
 Parameter: R -> "0.655506"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6.925258E-03" and "0.655506".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "6.925258E-03"
 Parameter: R -> "0.655506"
 Comparing "6.925258E-03" and "0.655506".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "2"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "4"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "2"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "2" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "8.843797E-02"
 Parameter: CHICHOICE1 <- "8.843797E-02"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "8.843797E-02"
 Parameter: BONDS -> "5"
Evaluating: INT(8.843797E-02*5)
 Parameter: CHICHOICE2 <- "0"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "0"
 Parameter: BONDS -> "5"
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "5"
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "0"
 Parameter: CHICHOICE2 -> "0"
 Comparing "0" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str::
 OPNLGU> Unit 25 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi5.str
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    25
 RDTITL> SET CHI 0.377014
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.471679"
 Parameter: CHI <- "0.471679"
  
 CHARMM>    CALC chi5 = (@chi*360) - 180.0
 Parameter: CHI -> "0.471679"
Evaluating: (0.471679*360)-180.0
 Parameter: CHI5 <- "-10.1956"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 @chi5
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5 -> "-10.1956"
               FOUND IN IC  568 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   25 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "5".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI5COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "5"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "5" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1466 ATOM PAIRS WERE FOUND FOR ATOM LIST
      126 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      7.09001      0.04830
MINI EXTERN>  *************    353.26683      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1470 ATOM PAIRS WERE FOUND FOR ATOM LIST
      124 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        10
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1465 ATOM PAIRS WERE FOUND FOR ATOM LIST
      127 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        12
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1451 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1423 ATOM PAIRS WERE FOUND FOR ATOM LIST
      136 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        16
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1383 ATOM PAIRS WERE FOUND FOR ATOM LIST
      147 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1368 ATOM PAIRS WERE FOUND FOR ATOM LIST
      146 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1363 ATOM PAIRS WERE FOUND FOR ATOM LIST
      148 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        20
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1355 ATOM PAIRS WERE FOUND FOR ATOM LIST
      145 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   4546.05658*************   1085.81977      0.13312
MINI INTERN>     1986.17258     57.45146      0.00000      7.91159      2.52105
MINI EXTERN>     2493.35382     -1.35391      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        21
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1345 ATOM PAIRS WERE FOUND FOR ATOM LIST
      149 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        23
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1322 ATOM PAIRS WERE FOUND FOR ATOM LIST
      143 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        28
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1291 ATOM PAIRS WERE FOUND FOR ATOM LIST
      145 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        29
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1285 ATOM PAIRS WERE FOUND FOR ATOM LIST
      148 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1269 ATOM PAIRS WERE FOUND FOR ATOM LIST
      145 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1213 ATOM PAIRS WERE FOUND FOR ATOM LIST
      138 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        38
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1202 ATOM PAIRS WERE FOUND FOR ATOM LIST
      134 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        39
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1189 ATOM PAIRS WERE FOUND FOR ATOM LIST
      134 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   1163.15480   3382.90179    102.36662      0.06409
MINI INTERN>      747.62785     81.75802      0.00000     10.44676      2.67357
MINI EXTERN>      323.11633     -2.46775      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1175 ATOM PAIRS WERE FOUND FOR ATOM LIST
      133 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1162 ATOM PAIRS WERE FOUND FOR ATOM LIST
      133 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        43
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1158 ATOM PAIRS WERE FOUND FOR ATOM LIST
      131 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        44
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1140 ATOM PAIRS WERE FOUND FOR ATOM LIST
      130 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        46
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1132 ATOM PAIRS WERE FOUND FOR ATOM LIST
      125 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1112 ATOM PAIRS WERE FOUND FOR ATOM LIST
      123 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1074 ATOM PAIRS WERE FOUND FOR ATOM LIST
      111 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60    193.54054    969.61426     33.14592      0.03086
MINI INTERN>       31.93760     86.44386      0.00000      9.95979      1.88565
MINI EXTERN>       65.24980     -1.93615      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        61
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1035 ATOM PAIRS WERE FOUND FOR ATOM LIST
      105 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        71
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1002 ATOM PAIRS WERE FOUND FOR ATOM LIST
      102 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80    100.06112     93.47942     13.58843      0.01486
MINI INTERN>       15.10522     43.50321      0.00000     11.87776      1.51777
MINI EXTERN>       30.08229     -2.02512      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        88
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      985 ATOM PAIRS WERE FOUND FOR ATOM LIST
      102 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     71.72764     28.33348      7.56387      0.00715
MINI INTERN>        9.74753     30.92524      0.00000     14.46059      1.38544
MINI EXTERN>       17.16447     -1.95563      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     60.12406     11.60358     10.61619      0.00827
MINI INTERN>        7.69138     26.21191      0.00000     15.38325      1.81053
MINI EXTERN>       10.87382     -1.84684      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       121
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      970 ATOM PAIRS WERE FOUND FOR ATOM LIST
       99 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      140     52.60611      7.51794      2.64214      0.00398
MINI INTERN>        6.28078     22.76755      0.00000     15.50658      2.27780
MINI EXTERN>        7.53184     -1.75843      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     47.94473      4.66138      5.93271      0.00460
MINI INTERN>        5.79840     20.53155      0.00000     15.21723      2.71246
MINI EXTERN>        5.37023     -1.68514      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     44.14890      3.79583      1.99960      0.00221
MINI INTERN>        4.65692     19.25704      0.00000     14.77958      3.01982
MINI EXTERN>        4.06118     -1.62564      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       188
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      951 ATOM PAIRS WERE FOUND FOR ATOM LIST
       99 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      200     41.29236      2.85653      1.82826      0.00256
MINI INTERN>        4.19467     17.97815      0.00000     14.38743      3.20173
MINI EXTERN>        3.11383     -1.58346      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     41.29236      2.85653      1.82826      0.00307
STPD INTERN>        4.19467     17.97815      0.00000     14.38743      3.20173
STPD EXTERN>        3.11383     -1.58346      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are      951 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      951 ATOM PAIRS WERE FOUND FOR ATOM LIST
       98 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     41.29236      2.85653      1.82826      0.00000
MINI INTERN>        4.19467     17.97815      0.00000     14.38743      3.20173
MINI EXTERN>        3.11383     -1.58346      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         3
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      938 ATOM PAIRS WERE FOUND FOR ATOM LIST
       93 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         6
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      931 ATOM PAIRS WERE FOUND FOR ATOM LIST
       93 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         9
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      915 ATOM PAIRS WERE FOUND FOR ATOM LIST
       94 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      907 ATOM PAIRS WERE FOUND FOR ATOM LIST
       96 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     10.35519     30.93717     15.94203      0.09298
MINI INTERN>        3.92960      3.90678      0.00000      9.93944      2.14597
MINI EXTERN>       -8.52292     -1.04368      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      896 ATOM PAIRS WERE FOUND FOR ATOM LIST
       98 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      5.30325      5.05194      2.43982      0.01469
MINI INTERN>        0.38840      3.61121      0.00000      9.56008      1.08195
MINI EXTERN>       -8.28616     -1.05223      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        45
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      929 ATOM PAIRS WERE FOUND FOR ATOM LIST
      100 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60      1.36030      3.94296      2.01517      0.01378
MINI INTERN>        0.23897      3.07776      0.00000      7.47512      0.93781
MINI EXTERN>       -9.09088     -1.27849      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        61
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      944 ATOM PAIRS WERE FOUND FOR ATOM LIST
      105 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        68
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      968 ATOM PAIRS WERE FOUND FOR ATOM LIST
      104 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        73
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      981 ATOM PAIRS WERE FOUND FOR ATOM LIST
      106 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -2.55677      3.91706      1.99773      0.01292
MINI INTERN>        0.14157      2.91053      0.00000      4.79184      0.44634
MINI EXTERN>       -9.64975     -1.19730      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        86
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1009 ATOM PAIRS WERE FOUND FOR ATOM LIST
      112 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     -3.97108      1.41432      1.35530      0.00727
MINI INTERN>        0.10295      2.38435      0.00000      4.26492      0.26847
MINI EXTERN>       -9.69888     -1.29290      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       105
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1028 ATOM PAIRS WERE FOUND FOR ATOM LIST
      112 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     -4.58460      0.61351      0.81889      0.00409
MINI INTERN>        0.08298      1.80321      0.00000      3.85888      0.28454
MINI EXTERN>       -9.37400     -1.24021      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -4.92334      0.33874      1.25289      0.00640
MINI INTERN>        0.11966      1.80502      0.00000      3.71191      0.27882
MINI EXTERN>       -9.64834     -1.19041      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       143
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1040 ATOM PAIRS WERE FOUND FOR ATOM LIST
      116 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -5.12143      0.19809      0.28948      0.00216
MINI INTERN>        0.08554      1.91558      0.00000      3.30918      0.35233
MINI EXTERN>       -9.68670     -1.09737      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     -5.15749      0.03606      0.10172      0.00073
MINI INTERN>        0.08489      1.87009      0.00000      3.37445      0.31986
MINI EXTERN>       -9.69510     -1.11167      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     -5.20242      0.04493      0.29193      0.00190
MINI INTERN>        0.07896      1.92558      0.00000      3.24441      0.28896
MINI EXTERN>       -9.64175     -1.09858      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      220     -5.28750      0.08508      0.47075      0.00297
MINI INTERN>        0.08155      1.98803      0.00000      2.94337      0.28225
MINI EXTERN>       -9.57536     -1.00734      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       232
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1057 ATOM PAIRS WERE FOUND FOR ATOM LIST
      123 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      240     -5.36460      0.07710      0.62271      0.00279
MINI INTERN>        0.09432      1.88996      0.00000      2.81473      0.25822
MINI EXTERN>       -9.50098     -0.92085      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      260     -5.43461      0.07001      0.28408      0.00157
MINI INTERN>        0.07720      1.96666      0.00000      2.65767      0.30270
MINI EXTERN>       -9.54853     -0.89030      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      280     -5.47777      0.04316      0.26208      0.00147
MINI INTERN>        0.08419      1.84513      0.00000      2.68617      0.28458
MINI EXTERN>       -9.51071     -0.86713      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      295     -5.49104      0.01327      0.09636      0.00046
ABNR INTERN>        0.08392      1.81982      0.00000      2.70133      0.26032
ABNR EXTERN>       -9.49319     -0.86325      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.49104"
 Comparing "-5.49104" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.49104"
 Comparing "-5.49104" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.49104"
 Comparing "-5.49104" and "-12.8655".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.49104"
 Comparing "-5.49104" and "-12.8655".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.502096"
 Parameter: R <- "0.502096"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.49104"
Evaluating: -5.49104--12.8655
 Parameter: DELE <- "7.37446"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "7.37446"
Evaluating: 1.00654*7.37446
 Parameter: BETADELE <- "7.42269"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "7.42269"
Evaluating: EXP(-7.42269)
 Parameter: DELN <- "5.975396E-04"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "5.975396E-04"
 Parameter: R -> "0.502096"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "5.975396E-04" and "0.502096".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "5.975396E-04"
 Parameter: R -> "0.502096"
 Comparing "5.975396E-04" and "0.502096".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "3"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "5"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "3"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "3" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.728433"
 Parameter: CHICHOICE1 <- "0.728433"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.728433"
 Parameter: BONDS -> "5"
Evaluating: INT(0.728433*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.771573
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.823122"
 Parameter: CHI <- "0.823122"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.823122"
Evaluating: (0.823122*360)-180.0
 Parameter: CHI3 <- "116.324"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "116.324"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1424 ATOM PAIRS WERE FOUND FOR ATOM LIST
      128 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000      5.79012      0.04830
MINI EXTERN>  *************     45.03436      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1426 ATOM PAIRS WERE FOUND FOR ATOM LIST
      129 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1418 ATOM PAIRS WERE FOUND FOR ATOM LIST
      138 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1378 ATOM PAIRS WERE FOUND FOR ATOM LIST
      150 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1337 ATOM PAIRS WERE FOUND FOR ATOM LIST
      146 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   4444.32068*************    295.90646      0.05547
MINI INTERN>     3399.90906     90.16605      0.00000      4.61850      0.31415
MINI EXTERN>      951.40615     -2.09323      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        26
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1299 ATOM PAIRS WERE FOUND FOR ATOM LIST
      146 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        27
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1289 ATOM PAIRS WERE FOUND FOR ATOM LIST
      147 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        31
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1269 ATOM PAIRS WERE FOUND FOR ATOM LIST
      142 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1260 ATOM PAIRS WERE FOUND FOR ATOM LIST
      145 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        34
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1254 ATOM PAIRS WERE FOUND FOR ATOM LIST
      139 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        37
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1230 ATOM PAIRS WERE FOUND FOR ATOM LIST
      141 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        39
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1226 ATOM PAIRS WERE FOUND FOR ATOM LIST
      142 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   2204.83336   2239.48732    200.94941      0.06409
MINI INTERN>     1632.82277     78.33206      0.00000     10.92965      2.45134
MINI EXTERN>      483.16555     -2.86801      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        42
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1204 ATOM PAIRS WERE FOUND FOR ATOM LIST
      141 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        44
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1196 ATOM PAIRS WERE FOUND FOR ATOM LIST
      137 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        47
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1168 ATOM PAIRS WERE FOUND FOR ATOM LIST
      138 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        49
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1160 ATOM PAIRS WERE FOUND FOR ATOM LIST
      136 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        52
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1119 ATOM PAIRS WERE FOUND FOR ATOM LIST
      135 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1084 ATOM PAIRS WERE FOUND FOR ATOM LIST
      119 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1072 ATOM PAIRS WERE FOUND FOR ATOM LIST
      122 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60    432.80325   1772.03011    103.89348      0.07406
MINI INTERN>      186.00665    137.47613      0.00000     11.87718      1.86481
MINI EXTERN>       97.38509     -1.80660      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        65
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1019 ATOM PAIRS WERE FOUND FOR ATOM LIST
      112 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        74
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      994 ATOM PAIRS WERE FOUND FOR ATOM LIST
      108 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80    141.85239    290.95086     50.89436      0.03566
MINI INTERN>       29.64678     58.45471      0.00000      9.56558      4.45891
MINI EXTERN>       42.19455     -2.46814      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        88
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      967 ATOM PAIRS WERE FOUND FOR ATOM LIST
      107 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     76.69561     65.15679      6.39096      0.00715
MINI INTERN>       10.37628     33.02717      0.00000      9.03467      4.92854
MINI EXTERN>       21.71078     -2.38183      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       111
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      941 ATOM PAIRS WERE FOUND FOR ATOM LIST
      104 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     61.64485     15.05076     10.41298      0.00827
MINI INTERN>        8.91123     27.05661      0.00000      8.77429      5.43272
MINI EXTERN>       13.77473     -2.30474      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     52.92695      8.71790      3.70576      0.00398
MINI INTERN>        6.65384     24.76734      0.00000      8.62292      5.57541
MINI EXTERN>        9.55431     -2.24688      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       156
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      920 ATOM PAIRS WERE FOUND FOR ATOM LIST
      101 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     47.28231      5.64464      3.72266      0.00460
MINI INTERN>        5.88074     22.71032      0.00000      8.46644      5.44644
MINI EXTERN>        7.01731     -2.23893      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     42.88684      4.39547      7.58322      0.00531
MINI INTERN>        5.42330     21.08076      0.00000      8.30725      5.20878
MINI EXTERN>        5.15887     -2.29212      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200     39.00607      3.88078      7.97147      0.00614
MINI INTERN>        4.96329     19.47646      0.00000      8.14956      4.93340
MINI EXTERN>        3.84546     -2.36209      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200     39.00607      3.88078      7.97147      0.00307
STPD INTERN>        4.96329     19.47646      0.00000      8.14956      4.93340
STPD EXTERN>        3.84546     -2.36209      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are      920 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      906 ATOM PAIRS WERE FOUND FOR ATOM LIST
      100 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0     38.98943      0.01664      6.54122      0.00000
MINI INTERN>        5.26224     19.05680      0.00000      8.13238      4.90793
MINI EXTERN>        3.99465     -2.36457      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      904 ATOM PAIRS WERE FOUND FOR ATOM LIST
       96 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step         8
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      896 ATOM PAIRS WERE FOUND FOR ATOM LIST
       96 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      886 ATOM PAIRS WERE FOUND FOR ATOM LIST
       94 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        18
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      889 ATOM PAIRS WERE FOUND FOR ATOM LIST
       94 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20      1.22907     37.76036      7.66127      0.03254
MINI INTERN>        0.96426      1.73233      0.00000      6.62392      0.36259
MINI EXTERN>       -7.81818     -0.63585      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        24
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      895 ATOM PAIRS WERE FOUND FOR ATOM LIST
       99 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        32
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      903 ATOM PAIRS WERE FOUND FOR ATOM LIST
      102 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -0.35051      1.57958      0.48625      0.00396
MINI INTERN>        0.11874      1.64685      0.00000      5.66208      0.09596
MINI EXTERN>       -7.56766     -0.30650      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      911 ATOM PAIRS WERE FOUND FOR ATOM LIST
      102 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      928 ATOM PAIRS WERE FOUND FOR ATOM LIST
       99 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -2.71547      2.36495      1.81422      0.01031
MINI INTERN>        0.16298      1.82922      0.00000      3.94910      0.07337
MINI EXTERN>       -8.38607     -0.34406      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        72
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      940 ATOM PAIRS WERE FOUND FOR ATOM LIST
       97 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        80
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      948 ATOM PAIRS WERE FOUND FOR ATOM LIST
       99 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80     -4.26722      1.55175      5.54809      0.00645
MINI INTERN>        0.54796      2.56715      0.00000      1.12890      0.34843
MINI EXTERN>       -8.21752     -0.64213      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -5.26051      0.99329      0.84107      0.00403
MINI INTERN>        0.09759      2.03066      0.00000      1.60639      0.11139
MINI EXTERN>       -8.46783     -0.63872      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -5.42663      0.16612      0.36309      0.00227
MINI INTERN>        0.08537      1.77783      0.00000      1.56414      0.10637
MINI EXTERN>       -8.29675     -0.66358      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -5.47748      0.05085      0.30966      0.00213
MINI INTERN>        0.09104      1.62445      0.00000      1.65112      0.08705
MINI EXTERN>       -8.24303     -0.68811      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      160     -5.52150      0.04402      0.13085      0.00072
MINI INTERN>        0.08746      1.66026      0.00000      1.61551      0.09160
MINI EXTERN>       -8.26654     -0.70979      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      162     -5.52328      0.00177      0.09085      0.00087
ABNR INTERN>        0.08494      1.65679      0.00000      1.61633      0.09139
ABNR EXTERN>       -8.26223     -0.71050      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.52328"
 Comparing "-5.52328" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.52328"
 Comparing "-5.52328" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-5.52328"
 Comparing "-5.52328" and "-12.8655".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.52328"
 Comparing "-5.52328" and "-12.8655".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.218345"
 Parameter: R <- "0.218345"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-5.52328"
Evaluating: -5.52328--12.8655
 Parameter: DELE <- "7.34222"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "7.34222"
Evaluating: 1.00654*7.34222
 Parameter: BETADELE <- "7.39024"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "7.39024"
Evaluating: EXP(-7.39024)
 Parameter: DELN <- "6.172477E-04"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "6.172477E-04"
 Parameter: R -> "0.218345"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "6.172477E-04" and "0.218345".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str::
 OPNLGU> Unit 37 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/reject.str
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "6.172477E-04"
 Parameter: R -> "0.218345"
 Comparing "6.172477E-04" and "0.218345".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    37
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement rejects by 1
 Parameter: REJECTS <- "4"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   37 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.0"
 Parameter: R -> "0.0"
 Comparing "0.0" and "0.0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "6"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "4"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "4" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.728251"
 Parameter: CHICHOICE1 <- "0.728251"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.728251"
 Parameter: BONDS -> "5"
Evaluating: INT(0.728251*5)
 Parameter: CHICHOICE2 <- "3"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "3"
 Parameter: BONDS -> "5"
 Comparing "3" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "3"
 Parameter: CHICHOICE2 -> "3"
 Comparing "3" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "3"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "2".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str::
 OPNLGU> Unit 23 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi3.str
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    23
 RDTITL> SET CHI 0.709021
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.508169"
 Parameter: CHI <- "0.508169"
  
 CHARMM>    CALC chi3 = (@chi*360) - 180.0
 Parameter: CHI -> "0.508169"
Evaluating: (0.508169*360)-180.0
 Parameter: CHI3 <- "2.94084"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 @chi3
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3 -> "2.94084"
               FOUND IN IC  566 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   23 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "3".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI3COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "3"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "3" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1860 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0***************************************      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     12.19590      0.04830
MINI EXTERN>  *************     -1.95601      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         7
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1858 ATOM PAIRS WERE FOUND FOR ATOM LIST
      194 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        11
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1826 ATOM PAIRS WERE FOUND FOR ATOM LIST
      195 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        14
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1756 ATOM PAIRS WERE FOUND FOR ATOM LIST
      201 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        15
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1731 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        19
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1697 ATOM PAIRS WERE FOUND FOR ATOM LIST
      198 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20   5373.76597*************    834.88203      0.05547
MINI INTERN>     1630.38188    583.15776      0.00000      7.40182     33.69278
MINI EXTERN>     3119.58158     -0.44986      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        27
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1653 ATOM PAIRS WERE FOUND FOR ATOM LIST
      191 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        40
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1613 ATOM PAIRS WERE FOUND FOR ATOM LIST
      183 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40   3183.03668   2190.72929    482.75992      0.02670
MINI INTERN>      836.51283    491.24372      0.00000      7.18840     17.06003
MINI EXTERN>     1831.44750     -0.41579      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        48
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1595 ATOM PAIRS WERE FOUND FOR ATOM LIST
      175 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        51
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1569 ATOM PAIRS WERE FOUND FOR ATOM LIST
      173 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        52
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1573 ATOM PAIRS WERE FOUND FOR ATOM LIST
      172 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        53
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1547 ATOM PAIRS WERE FOUND FOR ATOM LIST
      172 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        54
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1549 ATOM PAIRS WERE FOUND FOR ATOM LIST
      171 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        55
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1526 ATOM PAIRS WERE FOUND FOR ATOM LIST
      170 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        56
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1518 ATOM PAIRS WERE FOUND FOR ATOM LIST
      168 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        57
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1499 ATOM PAIRS WERE FOUND FOR ATOM LIST
      162 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1489 ATOM PAIRS WERE FOUND FOR ATOM LIST
      165 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        59
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1479 ATOM PAIRS WERE FOUND FOR ATOM LIST
      158 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        60
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1467 ATOM PAIRS WERE FOUND FOR ATOM LIST
      163 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60   1302.15454   1880.88214    290.56176      0.17774
MINI INTERN>      634.07796    436.74078      0.00000      7.96184      0.56733
MINI EXTERN>      223.44156     -0.63493      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        62
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1456 ATOM PAIRS WERE FOUND FOR ATOM LIST
      155 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        69
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1412 ATOM PAIRS WERE FOUND FOR ATOM LIST
      150 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        78
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1374 ATOM PAIRS WERE FOUND FOR ATOM LIST
      143 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       80    217.07330   1085.08124     45.51958      0.03566
MINI INTERN>       36.80521    103.58621      0.00000     13.57952      0.42360
MINI EXTERN>       64.52449     -1.84573      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        88
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1351 ATOM PAIRS WERE FOUND FOR ATOM LIST
      144 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        97
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1330 ATOM PAIRS WERE FOUND FOR ATOM LIST
      146 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100     84.28254    132.79076      9.70781      0.01717
MINI INTERN>        4.46424     33.65795      0.00000     12.38750      0.86617
MINI EXTERN>       35.02382     -2.11714      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       113
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1291 ATOM PAIRS WERE FOUND FOR ATOM LIST
      144 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      120     39.89663     44.38592      8.10736      0.00827
MINI INTERN>        3.33942     13.42662      0.00000      8.46048      0.39464
MINI EXTERN>       16.53362     -2.25816      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     23.43467     16.46195     11.95915      0.00955
MINI INTERN>        3.10049      8.00912      0.00000      6.95445      0.63786
MINI EXTERN>        7.00688     -2.27412      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       151
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1246 ATOM PAIRS WERE FOUND FOR ATOM LIST
      142 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     14.30290      9.13177      3.47953      0.00460
MINI INTERN>        0.78126      6.73725      0.00000      6.31110      0.97055
MINI EXTERN>        1.75294     -2.25020      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180     10.12619      4.17671      6.57088      0.00531
MINI INTERN>        0.81990      5.99810      0.00000      6.00381      1.22227
MINI EXTERN>       -1.69971     -2.21818      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200      7.11847      3.00772      1.61817      0.00256
MINI INTERN>        0.58927      5.42906      0.00000      5.89955      1.34703
MINI EXTERN>       -3.96714     -2.17931      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 STEEPD> Minimization exiting with number of steps limit (       200) exceeded.

STPD MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
STPD INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
STPD EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
STPD>      200      7.11847      3.00772      1.61817      0.00307
STPD INTERN>        0.58927      5.42906      0.00000      5.89955      1.34703
STPD EXTERN>       -3.96714     -2.17931      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    MINI ABNR STEP .02 TOLENR @vtol TOLGRD @gtol TOLITR 100 TOLSTP 0.0 NSTEP @abnrsteps NPRINT 20
 Parameter: VTOL -> "0.0"
 Parameter: GTOL -> "0.1"
 Parameter: ABNRSTEPS -> "2000"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are     1246 atom  pairs and     5776 atom  exclusions.
 There are        0 group pairs and     1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1222 ATOM PAIRS WERE FOUND FOR ATOM LIST
      139 GROUP PAIRS REQUIRED ATOM SEARCHES



 ABNER> An energy minimization has been requested.

 EIGRNG =    0.0005000   MINDIM =            5
 NPRINT =           20   NSTEP  =         2000
 PSTRCT =    0.0000000   SDSTP  =    0.0200000
 STPLIM =    1.0000000   STRICT =    0.1000000
 TOLFUN =    0.0000000   TOLGRD =    0.1000000
 TOLITR =          100   TOLSTP =    0.0000000
 FMEM   =    0.0000000
MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0      7.11847      3.00772      1.61817      0.00000
MINI INTERN>        0.58927      5.42906      0.00000      5.89955      1.34703
MINI EXTERN>       -3.96714     -2.17931      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step         4
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1179 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       20     -2.95237     10.07084      1.75506      0.01001
MINI INTERN>        0.40421      3.89753      0.00000      5.81402      1.50414
MINI EXTERN>      -13.11634     -1.45593      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        30
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1188 ATOM PAIRS WERE FOUND FOR ATOM LIST
      130 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40     -6.93546      3.98309      2.48905      0.01564
MINI INTERN>        0.25998      2.51016      0.00000      5.20959      0.34354
MINI EXTERN>      -13.78206     -1.47666      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        41
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1205 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

 UPDECI: Nonbond update at step        58
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1211 ATOM PAIRS WERE FOUND FOR ATOM LIST
      132 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       60     -9.81861      2.88315      1.28426      0.00881
MINI INTERN>        0.12631      1.37413      0.00000      3.92645      0.14268
MINI EXTERN>      -14.21173     -1.17646      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80    -11.15527      1.33666      0.86790      0.00496
MINI INTERN>        0.15241      1.39566      0.00000      2.76783      0.24802
MINI EXTERN>      -14.84794     -0.87126      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        86
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1188 ATOM PAIRS WERE FOUND FOR ATOM LIST
      123 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      100    -12.09138      0.93611      0.83162      0.00465
MINI INTERN>        0.13431      1.30963      0.00000      2.52599      0.12481
MINI EXTERN>      -15.60151     -0.58462      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120    -12.28661      0.19523      0.44743      0.00262
MINI INTERN>        0.11051      1.27759      0.00000      2.36625      0.11746
MINI EXTERN>      -15.56924     -0.58918      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140    -12.38754      0.10093      0.33293      0.00245
MINI INTERN>        0.10387      1.25691      0.00000      2.27618      0.09365
MINI EXTERN>      -15.56788     -0.55026      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       146
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     1205 ATOM PAIRS WERE FOUND FOR ATOM LIST
      126 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160    -12.57935      0.19182      0.44233      0.00230
MINI INTERN>        0.07502      1.17057      0.00000      2.12609      0.07252
MINI EXTERN>      -15.60257     -0.42099      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      180    -12.72160      0.14224      0.75191      0.00360
MINI INTERN>        0.07905      1.20489      0.00000      2.09591      0.04990
MINI EXTERN>      -15.80269     -0.34867      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      200    -12.78372      0.06212      0.13654      0.00073
MINI INTERN>        0.08445      1.19684      0.00000      2.13961      0.04759
MINI EXTERN>      -15.89059     -0.36162      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

 ABNER> Minimization exiting with gradient tolerance ( 0.1000000) satisfied.

ABNR MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
ABNR INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ABNR EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ABNR>      203    -12.78446      0.00075      0.09456      0.00048
ABNR INTERN>        0.08259      1.20044      0.00000      2.13932      0.04862
ABNR EXTERN>      -15.89353     -0.36189      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   31 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    OPEN READ UNIT 34 CARD NAME @strpath/metropsamp.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str::
 OPNLGU> Unit 34 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metropsamp.str
  
 CHARMM>    STREAM UNIT 34

                    INPUT STREAM SWITCHING TO UNIT    34
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET rmstol 0.05
 Parameter: RMSTOL <- "0.05"
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .LE. @elast THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.7845"
 Comparing "-12.7845" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF ?ENER .LE. @elast THEN STREAM UNIT 38
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-12.7845"
 Comparing "-12.7845" and "-12.8655".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF ?ENER .GT. @elast THEN OPEN READ UNIT 36 CARD NAME @strpath/metcrit.str
 Parameter: ELAST -> "-12.8655"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 RDCMND substituted energy or value "?ENER" to "-12.7845"
 Comparing "-12.7845" and "-12.8655".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str::
 OPNLGU> Unit 36 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/metcrit.str
  
 CHARMM>    IF ?ENER .GT. @elast THEN STREAM UNIT 36
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-12.7845"
 Comparing "-12.7845" and "-12.8655".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    36
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET r ?RAND
 RDCMND substituted energy or value "?RAND" to "0.788506"
 Parameter: R <- "0.788506"
  
 CHARMM>    CALC delE = ?ENER - @elast
 Parameter: ELAST -> "-12.8655"
 RDCMND substituted energy or value "?ENER" to "-12.7845"
Evaluating: -12.7845--12.8655
 Parameter: DELE <- "8.100033E-02"
  
 CHARMM>    CALC betadelE = @beta * @delE
 Parameter: BETA -> "1.00654"
 Parameter: DELE -> "8.100033E-02"
Evaluating: 1.00654*8.100033E-02
 Parameter: BETADELE <- "8.153006E-02"
  
 CHARMM>    CALC delN = exp(-@betadelE)
 Parameter: BETADELE -> "8.153006E-02"
Evaluating: EXP(-8.153006E-02)
 Parameter: DELN <- "0.921705"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   36 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @delN .LT. @r THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: DELN -> "0.921705"
 Parameter: R -> "0.788506"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.921705" and "0.788506".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @delN .LT. @r THEN STREAM UNIT 37
 Parameter: DELN -> "0.921705"
 Parameter: R -> "0.788506"
 Comparing "0.921705" and "0.788506".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @delN .GT. @r THEN OPEN READ UNIT 38 CARD NAME @strpath/dupcheck.str
 Parameter: DELN -> "0.921705"
 Parameter: R -> "0.788506"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.921705" and "0.788506".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str::
 OPNLGU> Unit 38 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/dupcheck.str
  
 CHARMM>    IF @delN .GT. @r THEN STREAM UNIT 38
 Parameter: DELN -> "0.921705"
 Parameter: R -> "0.788506"
 Comparing "0.921705" and "0.788506".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    38
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Loop to read frame in frames directory
 CHARMM>    ! and calculate rmsd between candidate structure
 CHARMM>    ! and frame in saved frames
 CHARMM>    SET frame 1
 Parameter: FRAME <- "1"
  
 CHARMM>    COOR COPY COMP
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>    LABEL READ
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "1"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame1.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame1.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for  1361 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1359.9581  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.855956
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.85596"
 Parameter: RMSD <- "9.85596"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.85596"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.85596" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.85596"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.85596" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.85596"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.85596" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "2"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "2"
 Parameter: ACCEPTS -> "11"
 Comparing "2" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "2"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame2.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame2.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:28      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1445.9100  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.162642
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.1626"
 Parameter: RMSD <- "10.1626"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.1626"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1626" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.1626"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1626" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.1626"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.1626" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "3"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "3"
 Parameter: ACCEPTS -> "11"
 Comparing "3" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "3"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame3.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame3.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:29      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1121.7228  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    8.951149
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "8.95115"
 Parameter: RMSD <- "8.95115"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "8.95115"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.95115" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "8.95115"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.95115" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "8.95115"
 Parameter: RMSTOL -> "0.05"
 Comparing "8.95115" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "4"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "4"
 Parameter: ACCEPTS -> "11"
 Comparing "4" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "4"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame4.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame4.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:30      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1655.0921  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.872942
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.8729"
 Parameter: RMSD <- "10.8729"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.8729"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.8729" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.8729"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.8729" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.8729"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.8729" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "5"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "5"
 Parameter: ACCEPTS -> "11"
 Comparing "5" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "5"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame5.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame5.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1356.5339  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    9.843540
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "9.84354"
 Parameter: RMSD <- "9.84354"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "9.84354"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84354" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "9.84354"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84354" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "9.84354"
 Parameter: RMSTOL -> "0.05"
 Comparing "9.84354" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "6"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "6"
 Parameter: ACCEPTS -> "11"
 Comparing "6" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "6"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame6.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame6.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:32      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS   1419.5749  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS   10.069668
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "10.0697"
 Parameter: RMSD <- "10.0697"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "10.0697"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0697" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "10.0697"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0697" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "10.0697"
 Parameter: RMSTOL -> "0.05"
 Comparing "10.0697" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "7"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "7"
 Parameter: ACCEPTS -> "11"
 Comparing "7" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "7"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame7.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame7.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    173.6263  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.521630
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.52163"
 Parameter: RMSD <- "3.52163"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.52163"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52163" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.52163"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52163" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.52163"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.52163" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "8"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "8"
 Parameter: ACCEPTS -> "11"
 Comparing "8" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "8"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame8.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame8.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:33      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    154.0455  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    3.317115
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "3.31711"
 Parameter: RMSD <- "3.31711"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "3.31711"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.31711" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "3.31711"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.31711" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "3.31711"
 Parameter: RMSTOL -> "0.05"
 Comparing "3.31711" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "9"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "9"
 Parameter: ACCEPTS -> "11"
 Comparing "9" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "9"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame9.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame9.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:34      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS    393.7829  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    5.303523
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "5.30352"
 Parameter: RMSD <- "5.30352"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "5.30352"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.30352" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "5.30352"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.30352" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "5.30352"
 Parameter: RMSTOL -> "0.05"
 Comparing "5.30352" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "10"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "10"
 Parameter: ACCEPTS -> "11"
 Comparing "10" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "10"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame10.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame10.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:34      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS     88.0755  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    2.508209
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "2.50821"
 Parameter: RMSD <- "2.50821"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "2.50821"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.50821" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "2.50821"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.50821" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "2.50821"
 Parameter: RMSTOL -> "0.05"
 Comparing "2.50821" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "11"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "11"
 Parameter: ACCEPTS -> "11"
 Comparing "11" and "11".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 53 CARD NAME @frameout/frame@frame.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: FRAME -> "11"
 OPNLGU> Unit already open. The old file will be closed first.
 VCLOSE: Closing unit   53 with status "KEEP"
 VOPEN> Attempting to open::frames/frame11.crd::
 OPNLGU> Unit 53 opened for READONLY access to frames/frame11.crd
  
 CHARMM>    READ COOR UNIT 53 CARD
          SPATIAL COORDINATES BEING READ FROM UNIT 53
 TITLE> * ". "
 TITLE> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 TITLE> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 TITLE> *  DATE:     6/15/ 6     14:53:35      CREATED BY USER: FAJER
 TITLE> *

 ** WARNING ** Coordinates were overwritten for    14 atoms.
 *** LEVEL  2 WARNING *** BOMLEV IS   -2
  
 CHARMM>    !COOR RMS SELE RESID @labresid END
 CHARMM>    COOR RMS SELE moveset END
 SELRPN>     14 atoms have been selected out of   1361
 TOTAL SQUARE DIFF IS     29.6195  DENOMINATOR IS     14.0000
       THUS RMS DIFF IS    1.454537
 RMS FOUND FOR SELECTED COORDINATES WITHOUT ROTATION
  
 CHARMM>    SET rmsd ?RMS
 RDCMND substituted energy or value "?RMS" to "1.45454"
 Parameter: RMSD <- "1.45454"
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN COOR SWAP      ! A duplicate was found; swap coords back
 Parameter: RMSD -> "1.45454"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.45454" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN INCR dups BY 1 ! A duplicate was found; incriment counter
 Parameter: RMSD -> "1.45454"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.45454" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN RETURN         ! A duplicate was found; reject
 Parameter: RMSD -> "1.45454"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.45454" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    INCR frame by 1
 Parameter: FRAME <- "12"
  
 CHARMM>    IF @frame .LE. @accepts GOTO READ
 Parameter: FRAME -> "12"
 Parameter: ACCEPTS -> "11"
 Comparing "12" and "11".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    SET dups 0           ! No duplicate found; reset counter
 Parameter: DUPS <- "0"
  
 CHARMM>    COOR SWAP
 SELECTED COORDINATES SWAPPED.

  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   38 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>     
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN OPEN READ UNIT 35 CARD NAME @strpath/accept.str
 Parameter: RMSD -> "1.45454"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1.45454" and "0.05".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str::
 OPNLGU> Unit 35 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/accept.str
  
 CHARMM>    IF @rmsd .GT. @rmstol THEN STREAM UNIT 35
 Parameter: RMSD -> "1.45454"
 Parameter: RMSTOL -> "0.05"
 Comparing "1.45454" and "0.05".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    35
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    INCRement accepts by 1
 Parameter: ACCEPTS <- "12"
  
 CHARMM>    OPEN READ UNIT 33 CARD NAME @strpath/output.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str::
 OPNLGU> Unit 33 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/output.str
  
 CHARMM>    STREAM UNIT 33

                    INPUT STREAM SWITCHING TO UNIT    33
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    IF @accepts .EQ. 1 THEN OPEN READ UNIT 81 CARD NAME @strpath/frame1out.str
 Parameter: ACCEPTS -> "12"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "12" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @accepts .EQ. 1 THEN STREAM UNIT 81
 Parameter: ACCEPTS -> "12"
 Comparing "12" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @accepts .NE. 1 THEN OPEN READ UNIT 82 CARD NAME @strpath/frameout.str
 Parameter: ACCEPTS -> "12"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "12" and "1".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str::
 OPNLGU> Unit 82 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/frameout.str
  
 CHARMM>    IF @accepts .NE. 1 THEN STREAM UNIT 82
 Parameter: ACCEPTS -> "12"
 Comparing "12" and "1".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    82
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 51 CARD NAME @frameout/frame@accepts.crd
 Parameter: FRAMEOUT -> "FRAMES"
 Parameter: ACCEPTS -> "12"
 VOPEN> Attempting to open::frames/frame12.crd::
 OPNLGU> Unit 51 opened for WRITE access to frames/frame12.crd
  
 CHARMM>    !WRITE COOR UNIT 51 CARD SELE RESID @labresid END
 CHARMM>    WRITE COOR UNIT 51 CARD SELE moveset END
 RDTITL> * ". "
 RDTITL> * MMC-MINIMIZATION USING SD AND ABNR MINIMIZATION
 RDTITL> * COORDINATS OF CMTS SAVED AT AN ENERGY MINIMA
 RDTITL> *
 SELRPN>     14 atoms have been selected out of   1361
 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED

 VCLOSE: Closing unit   51 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   82 with status "KEEP"

                    RETURNING TO INPUT STREAM    33
  
 CHARMM>     
  
 CHARMM>    OPEN WRITE UNIT 52 CARD APPEND NAME mmcm.ene
 VOPEN> Attempting to open::mmcm.ene::
 OPNLGU> Unit 52 opened for APPEND access to mmcm.ene
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 WRITE
  
 CHARMM>    WRITE TITLE UNIT 52
 RDTITL> * -12.7845 8.258949E-02 1.20044 2.13932 -15.8935 -0.361893
 RDTITL> *
  
 CHARMM>    CLOSE UNIT 52
 VCLOSE: Closing unit   52 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   33 with status "KEEP"

                    RETURNING TO INPUT STREAM    35
  
 CHARMM>    SET elast ?ENER
 RDCMND substituted energy or value "?ENER" to "-12.7845"
 Parameter: ELAST <- "-12.7845"
  
 CHARMM>    SET r 0.0
 Parameter: R <- "0.0"
  
 CHARMM>    SET delN 0.0
 Parameter: DELN <- "0.0"
  
 CHARMM>    SET rmsd @rmstol
 Parameter: RMSTOL -> "0.05"
 Parameter: RMSD <- "0.05"
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   35 with status "KEEP"

                    RETURNING TO INPUT STREAM    34
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN OPEN READ UNIT 37 CARD NAME @strpath/reject.str
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @rmsd .LT. @rmstol THEN STREAM UNIT 37
 Parameter: RMSD -> "0.05"
 Parameter: RMSTOL -> "0.05"
 Comparing "0.05" and "0.05".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   34 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>     
  
 CHARMM>    ! The number of iterations counter is incremented and
 CHARMM>    ! control is returned to the begining of the MC loop
 CHARMM>    INCRement iterations by 1
 Parameter: ITERATIONS <- "7"
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   20 with status "KEEP"

                    RETURNING TO INPUT STREAM    19
  
 CHARMM>    IF @dups .LT. @maxdups THEN IF @rejects .LT. @maxrejects THEN GOTO mcloop
 Parameter: DUPS -> "0"
 Parameter: MAXDUPS -> "20"
 Parameter: REJECTS -> "4"
 Parameter: MAXREJECTS -> "20"
 Comparing "0" and "20".
 IF test evaluated as true.  Performing command
 Comparing "4" and "20".
 IF test evaluated as true.  Performing command
  
 CHARMM>    OPEN READ UNIT 20 CARD NAME @strpath/mc.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str::
 OPNLGU> Unit 20 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/mc.str
  
 CHARMM>    STREAM UNIT 20

                    INPUT STREAM SWITCHING TO UNIT    20
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    SET chi1count = 0
 Parameter: CHI1COUNT <- "0"
  
 CHARMM>    SET chi2count = 0
 Parameter: CHI2COUNT <- "0"
  
 CHARMM>    SET chi3count = 0
 Parameter: CHI3COUNT <- "0"
  
 CHARMM>    SET chi4count = 0
 Parameter: CHI4COUNT <- "0"
  
 CHARMM>    SET chi5count = 0
 Parameter: CHI5COUNT <- "0"
  
 CHARMM>    SET chi6count = 0
 Parameter: CHI6COUNT <- "0"
  
 CHARMM>    SET chi7count = 0
 Parameter: CHI7COUNT <- "0"
  
 CHARMM>    SET numchosen = 0
 Parameter: NUMCHOSEN <- "0"
  
 CHARMM>     
  
 CHARMM>    LABEL perturb
  
 CHARMM>     
  
 CHARMM>    SET chichoice1 = ?RAND
 RDCMND substituted energy or value "?RAND" to "0.427827"
 Parameter: CHICHOICE1 <- "0.427827"
  
 CHARMM>    CALC chichoice2 = int(@chichoice1*@bonds)	! this truncates giving chichoice E[0,bonds-1]
 Parameter: CHICHOICE1 -> "0.427827"
 Parameter: BONDS -> "5"
Evaluating: INT(0.427827*5)
 Parameter: CHICHOICE2 <- "2"
  
 CHARMM>    IF @chichoice2 .EQ. 0 THEN SET chichoice @bonds ! so if 0 then make it last bond
 Parameter: CHICHOICE2 -> "2"
 Parameter: BONDS -> "5"
 Comparing "2" and "0".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chichoice2 .NE. 0 THEN SET chichoice @chichoice2
 Parameter: CHICHOICE2 -> "2"
 Parameter: CHICHOICE2 -> "2"
 Comparing "2" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHICHOICE <- "2"
  
 CHARMM>     
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN OPEN READ UNIT 21 CARD NAME @strpath/randchi1.str
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN STREAM UNIT 21
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi1change .EQ. 1 THEN IF @chichoice .EQ. 1 THEN IF @chi1count .EQ. 0 THEN SET chi1count 1
 Parameter: CHI1CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI1COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN OPEN READ UNIT 22 CARD NAME @strpath/randchi2.str
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str::
 OPNLGU> Unit 22 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/randchi2.str
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN STREAM UNIT 22
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command

                    INPUT STREAM SWITCHING TO UNIT    22
 RDTITL> SET CHI 0.495814
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    SET chi ?RAND
 RDCMND substituted energy or value "?RAND" to "0.151048"
 Parameter: CHI <- "0.151048"
  
 CHARMM>    CALC chi2 = (@chi*360) - 180.0
 Parameter: CHI -> "0.151048"
Evaluating: (0.151048*360)-180.0
 Parameter: CHI2 <- "-125.623"
  
 CHARMM>    !
 CHARMM>    IC EDIT
  
 EDITIC>      DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 @chi2
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2 -> "-125.623"
               FOUND IN IC  565 AS POSITIVE
  
 EDITIC>    END
  
 CHARMM>    COOR INIT SELE spinset END
 SELRPN>     14 atoms have been selected out of   1361
 SELECTED COORDINATES INITIALIZED IN THE MAIN SET.

  
 CHARMM>    IC BUILd  ! rebuild the cartesian coordiantes
 ALL POSSIBLE COORDINATES HAVE BEEN PLACED
  
 CHARMM>     
  
 CHARMM>    RETURN
 VCLOSE: Closing unit   22 with status "KEEP"

                    RETURNING TO INPUT STREAM    20
  
 CHARMM>    IF @chi2change .EQ. 1 THEN IF @chichoice .EQ. 2 THEN IF @chi2count .EQ. 0 THEN SET chi2count 1
 Parameter: CHI2CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI2COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "2".
 IF test evaluated as true.  Performing command
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CHI2COUNT <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN OPEN READ UNIT 23 CARD NAME @strpath/randchi3.str
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN STREAM UNIT 23
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3change .EQ. 1 THEN IF @chichoice .EQ. 3 THEN IF @chi3count .EQ. 0 THEN SET chi3count 1
 Parameter: CHI3CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI3COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "3".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN OPEN READ UNIT 24 CARD NAME @strpath/randchi4.str
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN STREAM UNIT 24
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4change .EQ. 1 THEN IF @chichoice .EQ. 4 THEN IF @chi4count .EQ. 0 THEN SET chi4count 1
 Parameter: CHI4CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI4COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "4".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi5.str
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5change .EQ. 1 THEN IF @chichoice .EQ. 5 THEN IF @chi5count .EQ. 0 THEN SET chi5count 1
 Parameter: CHI5CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI5COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "5".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi6.str
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6change .EQ. 1 THEN IF @chichoice .EQ. 6 THEN IF @chi6count .EQ. 0 THEN SET chi6count 1
 Parameter: CHI6CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI6COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "6".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN OPEN READ UNIT 25 CARD NAME @strpath/randchi7.str
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN STREAM UNIT 25
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7change .EQ. 1 THEN IF @chichoice .EQ. 7 THEN IF @chi7count .EQ. 0 THEN SET chi7count 1
 Parameter: CHI7CHANGE -> "1"
 Parameter: CHICHOICE -> "2"
 Parameter: CHI7COUNT -> "0"
 Comparing "1" and "1".
 IF test evaluated as true.  Performing command
 Comparing "2" and "7".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    INCRement numchosen by 1
 Parameter: NUMCHOSEN <- "1"
  
 CHARMM>     
  
 CHARMM>    IF @numchosen .LT. @numrotate THEN GOTO perturb
 Parameter: NUMCHOSEN -> "1"
 Parameter: NUMROTATE -> "1"
 Comparing "1" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    ! Once torsion angles are altered the minimization stream file
 CHARMM>    ! is called (UNIT 31) and control is returned to this file
 CHARMM>    ! Then the metropsamp stream (UNIT 34) is called to determine
 CHARMM>    ! whether or not the new structure is accpted.
 CHARMM>    OPEN READ UNIT 31 CARD NAME @strpath/minimize.str
 Parameter: STRPATH -> "$SL_MOD/CHARMM/CHARMM_MMCM_STR"
 VOPEN> Attempting to open::/home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str::
 OPNLGU> Unit 31 opened for READONLY access to /home/fajer/sl_mod/charmm/charmm_mmcm_str/minimize.str
  
 CHARMM>    STREAM UNIT 31

                    INPUT STREAM SWITCHING TO UNIT    31
 RDTITL> 
 RDTITL> No title read.
 Parameter: IN1 <- "" <empty>
  
 CHARMM>     
  
 CHARMM>    ! Fix all atoms other than those selected in moveset in setglobals.str during minimization
 CHARMM>    CONS FIX SELE .NOT. moveset PURG END
 CSTRAN: Irreversible compression of PSF is performed.
 SELRPN>   1347 atoms have been selected out of   1361
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =      136
         Number of atoms         =     1361   Number of groups     =      521
         Number of bonds         =     1383   Number of angles     =       25
         Number of dihedrals     =        8   Number of impropers  =        2
         Number of HB acceptors  =      203   Number of HB donors  =      261
         Number of NB exclusions =       66   Total charge =    9.00000
  
 CHARMM>     
  
 CHARMM>    IF @chi1conb .EQ. 1 THEN CONS DIHE @labresno @chi1atom1 @labresno @chi1atom2 @labresno @chi1atom3 @labresno @chi1atom4 FORCE @chi1conf MIN @chi1conv
 Parameter: CHI1CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM1 -> "N"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM2 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM3 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI1ATOM4 -> "SG"
 Parameter: CHI1CONF -> "0.0"
 Parameter: CHI1CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi2conb .EQ. 1 THEN CONS DIHE @labresno @chi2atom1 @labresno @chi2atom2 @labresno @chi2atom3 @labresno @chi2atom4 FORCE @chi2conf MIN @chi2conv
 Parameter: CHI2CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM1 -> "CA"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM2 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM3 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI2ATOM4 -> "S1"
 Parameter: CHI2CONF -> "0.0"
 Parameter: CHI2CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi3conb .EQ. 1 THEN CONS DIHE @labresno @chi3atom1 @labresno @chi3atom2 @labresno @chi3atom3 @labresno @chi3atom4 FORCE @chi3conf MIN @chi3conv
 Parameter: CHI3CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM1 -> "CB"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM2 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM3 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI3ATOM4 -> "C10"
 Parameter: CHI3CONF -> "0.0"
 Parameter: CHI3CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi4conb .EQ. 1 THEN CONS DIHE @labresno @chi4atom1 @labresno @chi4atom2 @labresno @chi4atom3 @labresno @chi4atom4 FORCE @chi4conf MIN @chi4conv
 Parameter: CHI4CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM1 -> "SG"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM2 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM3 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI4ATOM4 -> "C3"
 Parameter: CHI4CONF -> "0.0"
 Parameter: CHI4CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi5conb .EQ. 1 THEN CONS DIHE @labresno @chi5atom1 @labresno @chi5atom2 @labresno @chi5atom3 @labresno @chi5atom4 FORCE @chi5conf MIN @chi5conv
 Parameter: CHI5CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM1 -> "S1"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM2 -> "C10"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM3 -> "C3"
 Parameter: LABRESNO -> "59"
 Parameter: CHI5ATOM4 -> "C2"
 Parameter: CHI5CONF -> "0.0"
 Parameter: CHI5CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi6conb .EQ. 1 THEN CONS DIHE @labresno @chi6atom1 @labresno @chi6atom2 @labresno @chi6atom3 @labresno @chi6atom4 FORCE @chi6conf MIN @chi6conv
 Parameter: CHI6CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI6ATOM4 -> "DUMMY"
 Parameter: CHI6CONF -> "0.0"
 Parameter: CHI6CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>    IF @chi7conb .EQ. 1 THEN CONS DIHE @labresno @chi7atom1 @labresno @chi7atom2 @labresno @chi7atom3 @labresno @chi7atom4 FORCE @chi7conf MIN @chi7conv
 Parameter: CHI7CONB -> "0"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM1 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM2 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM3 -> "DUMMY"
 Parameter: LABRESNO -> "59"
 Parameter: CHI7ATOM4 -> "DUMMY"
 Parameter: CHI7CONF -> "0.0"
 Parameter: CHI7CONV -> "0.0"
 Comparing "0" and "1".
 IF test evaluated as false.  Skipping command
  
 CHARMM>     
  
 CHARMM>    MINI SD STEP .02 NSTEP @sdsteps NPRINT 20
 Parameter: SDSTEPS -> "200"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    RDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 11.000 CTEXNB =999.000 CTONNB =  9.000 CTOFNB = 10.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  2.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found   3418 exclusions and   2358 interactions(1-4)
 <MAKGRP> found   1324 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2105 ATOM PAIRS WERE FOUND FOR ATOM LIST
      215 GROUP PAIRS REQUIRED ATOM SEARCHES



 STEEPD> An energy minimization has been requested.

 NSTEP  =          200   NPRINT =           20
 STEP   =    0.0200000   TOLFUN =    0.0000000
 TOLGRD =    0.0000000   TOLSTP =    0.0000000

MINI MIN: Cycle      ENERgy      Delta-E         GRMS    Step-size
MINI INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
MINI EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>        0    121.66787   -134.45233     63.55396      0.02000
MINI INTERN>       15.35281      6.64424      0.00000     10.69487      0.04830
MINI EXTERN>       89.41418     -0.48654      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       20     16.96178    104.70609     12.20618      0.00963
MINI INTERN>        1.07687      7.25716      0.00000      7.80085      0.41465
MINI EXTERN>        1.04031     -0.62807      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step        22
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2076 ATOM PAIRS WERE FOUND FOR ATOM LIST
      212 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>       40      6.42800     10.53378      2.70642      0.00464
MINI INTERN>        0.12576      5.63827      0.00000      6.28475      0.58640
MINI EXTERN>       -5.46908     -0.73809      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       60      2.17570      4.25230      6.32791      0.00536
MINI INTERN>        0.49272      5.08481      0.00000      5.50357      0.63559
MINI EXTERN>       -8.74133     -0.79966      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>       80     -0.60851      2.78421      2.18560      0.00258
MINI INTERN>        0.06816      4.81184      0.00000      5.13456      0.61959
MINI EXTERN>      -10.40545     -0.83721      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      100     -2.26189      1.65338      3.85405      0.00298
MINI INTERN>        0.14536      4.57178      0.00000      4.88085      0.57209
MINI EXTERN>      -11.56418     -0.86779      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      120     -3.45903      1.19713      4.33084      0.00344
MINI INTERN>        0.15464      4.38528      0.00000      4.68998      0.52239
MINI EXTERN>      -12.31955     -0.89178      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
MINI>      140     -4.59447      1.13544      1.15956      0.00166
MINI INTERN>        0.06770      4.19305      0.00000      4.52095      0.47363
MINI EXTERN>      -12.93800     -0.91180      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
 UPDECI: Nonbond update at step       147
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR   189699 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
     2010 ATOM PAIRS WERE FOUND FOR ATOM LIST
      215 GROUP PAIRS REQUIRED ATOM SEARCHES

MINI>      160     -5.46904      0.87458      2.25038      0.00192
MINI INTERN>        0.11990      4.01912      0.00000      4.34397      0.42746
MINI EXTERN>      -13.44713     -0.93238      0.00000      0.00000      0.00000
 ----------       ----