AMBER Archive (2007)

Subject: Re: AMBER: explanation to edit and use the script

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Wed Jun 20 2007 - 04:33:15 CDT

--- Syed Tarique Moin <tarisyed_at_yahoo.com> wrote:

> 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"
>
>

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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