AMBER: New 2 the board

From: Campbell, Patrick <>
Date: Wed, 12 Dec 2007 16:12:30 -0500

Hello all,
I am a student and I have recently started the usage of AMBER for protein optimization. The question that I have might have a straightforward response so do bear with me.
I have created an input file ( for the optimization of my protein. file:
#PBS -S /bin/csh
#PBS -l cput=10:00:00
#PBS -l ncpus=2
setenv LD_LIBRARY_PATH /opt/cmplrs/8.0.046/lib/:/opt/cmplrs/8.0.066/lib
setenv NCPUS 2
setenv AMBERHOME /usr/local/appl/Amber8
set path = ( $path $AMBERHOME/exe )
cd /ptmp/$USER/amber
mpirun -np $NCPUS $AMBERHOME/exe/sander -O -i -p TC5b.prmtop -c heat7.rst -r equil1.rst -o equil1.out -x equil1.mdcrd

where cput - time in hours:min:sec
       ncpus and NCPUS - number of CPUs

My PDB protein is saved in my working directory under the name LTR. I have also saved the input file (shown above) under the name - I thus have two files in my working directory.

I would like to optimize the PDB file and would like to know how the link between the input file and the PDB file is made.

What I would like to know is

a. If the file name has to be entered into the input file for the job to run or

b. If the data from the PDB file has to be copied into the input file before the job is run.

Any assistance in bringing clarity to this matter is deeply appreciated.


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Received on Sun Dec 16 2007 - 06:07:09 PST
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