Guide to Biomolecular Simulations, Becker & Karplus
 (Date: February 28, 2006)


General directive to copying the CD

For compatibility purposes the files on this CD were saved from a Windows XP operating system. After copying the files to a UNIX machine you will need to run the to_unix command which reformats the files so that they are compatible with the UNIX operating system. This command should be executed for each file on the CD.

1. To executed this command for the individual file filename:
	
> to_unix  filename  filename


2. To execute this command for all the files in a certain directory dirname: 

> cd dirname 
> foreach i (*)

This will open a foreach session, characterizes by the prompt "foreach?",

foreach?  to_unix $i $i
foreach?  echo $i
foreach?  end


Corrections and Updates

Lab 4 (p. 66 in "PROCEDURE")

In the lab4 directory you will find three files and a subdirectory named lib, which contains two files.

Lab 5 (p. 86, 88, 91, 92)
The awk script logDE.awk is no longer provided with Lab 5.  Hence the lab5 directory contains only eight files plus the lib subdirectory.

The stability calculations should be performed using available tools (e.g., Excel) according to the following formula:

Average of E = <E>
Average fluctuation of E = <DE> = (1/n)SUMn(Ei - <E>)
logDE = log10(|<DE>/<E>|)


Lab 9 (p. 179)

The two awk scripts pert.awk & pert1.awk were moved from the data subdirectory to the main lib9 directory.

Lab 11 (p. 211)

The construct program that is supplied with the Guide and creates the repl1.crd coordinate file, does not work on all computer architectures.

If this program does not work on your computer simply use the repl1.crd file given in the construct sub-directory.


