AMBER Archive (2007)

Subject: AMBER: explanation to edit and use the script

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Sun Jun 17 2007 - 23:26:38 CDT

Hello,
   
  I have attached file script of DNA simulation for 1.8 ns, I want to use it for my own purpose for the protein, kindly explain the restraint energy for md simulation input file in which 10 kcal is used.
   
  Regards

Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com
 
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#!/bin/csh
set AMBERHOME="/usr/local/AMBER8"
set MDSTARTJOB=2
set MDENDJOB=10
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=0

echo -n "Starting Script at: "
date
echo ""

while ( $MDCURRENTJOB <= $MDENDJOB )
   echo -n "Job $MDCURRENTJOB started at: "
   date
   @ MDINPUT = $MDCURRENTJOB - 1
   $AMBERHOME/exe/sander -O -i a-dna_md_1800ps.in \
                            -o a-dna_md$MDCURRENTJOB.out \
                            -p a-dna_wat.prmtop \
                            -c a-dna_md$MDINPUT.rst \
                            -r a-dna_md$MDCURRENTJOB.rst \
                            -x a-dna_md$MDCURRENTJOB.mdcrd
   gzip -9 -v a-dna_md$MDCURRENTJOB.mdcrd
   echo -n "Job $MDCURRENTJOB finished at: "
   date
   @ MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"

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