#!/bin/sh

echo '**********************************************************************'
echo ' Pulls out coordinates of 1 or 2 spin labels from MD trajectory'
echo '**********************************************************************'

# Assign start values to variables 
probe="CMTS"
	echo $probe
crdroot="build"
	echo $crdroot
psfroot="build"
	echo $psfroot
dcdroot="prod"

	numframes=`awk 'END{print(NR-3)}' $dcdroot.ene`
	echo frames $numframes
	
	awk '/CMTS/ && /SG/ {print $8 " " $9}' $crdroot.crd > label.txt
	labelsegid1=`awk 'NR==1 {print $1}' label.txt`
	labelresid1=`awk 'NR==1 {print $2}' label.txt`
# un-supress the lines if you know the label residue id and segment id's
#labelsegid1=??
#labelresid1=??
	echo label_1 $labelresid1 "  " segment $labelsegid1;
	labelsegid2=`awk 'NR==2 {print $1}' label.txt`
	labelresid2=`awk 'NR==2 {print $2}' label.txt`;
#labelsegid2=??
#labelresid2=??
	echo label_2 $labelresid2 "  " segment $labelsegid2;

	charmm < $SL_MOD/charmm/charmm_md/spin_spin.inp numframes="$numframes" labresid1="$labelresid1" labsegid1="$labelsegid1" labresid2="$labelresid2" labsegid2="$labelsegid2" crdroot="$crdroot" psfroot="$psfroot" dcdroot="$dcdroot" firsttime="$first" lasttime="$numframes" skiptime="$skip"  > gettcno.out
	
	awk 'NR>16 {print}' ccnoa.dat > ccnoa1.data
	awk 'NR>16 {print}' ccnob.dat > ccnob1.data
	awk 'NR>16 {print}' ccnoc.dat > ccnoc1.data
	
	

        cut -c10-116 ccnoa1.data > ccnoa.data
#change the following line if any problems with smaller lables
        cut -c10-116 ccnob1.data > ccnob.data
        cut -c10-80 ccnoc1.data > ccnoc.data
        paste ccnoa.data ccnob.data ccnoc.data > $dcdroot.dat
        cut -c26-33 $dcdroot.ene > $dcdroot.time
	rm ccnoa1.data ccnob1.data ccnoa.data ccnob.data ccnoc1.data ccnoc.dat

