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.yahoo.com
tarisyed.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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Received on Wed Jun 20 2007 - 06:07:14 PDT
