Re: [AMBER] Running a small minimization with amber 16 package

From: Debarati DasGupta <>
Date: Tue, 31 Jul 2018 21:51:56 +0000

That is the output.

-rw-r--r-- 1 ohu0513 PHS0297 885812 Jul 31 12:15 min_restrain.rst

The file min_restrain.rst is definitely present and I used cpptraj to convert it to a Amber restart.

Can you help me understand what is the issue?

The script I am using is given here. I routinely run amber 12 and this error has not happened before.

#PBS -l walltime=1:00:00
#(wall time of 100 hours)

#PBS -l nodes=1:ppn=12:gpus=1
#(use of 1 node, 1 processors)

#PBS -N 1J2F_amber
#(job name=quat-16_bulk)

#PBS -A PHS0297

echo job on compute node 'cat $PBS_NODEFILE'
cp $TMPDIR #copies files to home directory
cp t.pdb $TMPDIR

cp *.in $TMPDIR
cp Protein.* $TMPDIR
#module load intel/15.0.3
#module load mvapich2/2.1
module load amber
module load cuda
#tleap -f
#cp *.pdb *.top *.crd $PBS_O_WORKDIR #copies output results back to home directory

pmemd.cuda -O -i -o min_restrain.out -c Protein.crd -p -r min_restrain.rst -ref Protein.crd

pmemd.cuda -O -i -o min.out -c output.rst -p -r min.rst

pmemd.cuda -O -i -o heat.out -c min_restrain.rst -p -r heat.rst -x heat.mdcrd -ref min_restrain.rst

pmemd.cuda -O -i -o prod.out -c heat.rst -p -r prod.rst -x prod.mdcrd -ref heat.rst

cp *out *.rst *.mdcrd $PBS_O_WORKDIR

The one coded in green is working well.
The one coded in blue color is giving error that min_restrain.rst error on opening.
From: David A Case <>
Sent: Wednesday, August 1, 2018 12:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Running a small minimization with amber 16 package

On Tue, Jul 31, 2018, Debarati DasGupta wrote:
> Unit 9 Error on OPEN: min_restrain.rst

What are the results of the following commands?

   ls -l min_restrain.rst
   file min_restrain.rst

Usually, an open error means the file is not present, or you do not have
permissions to read it. The format of the file should not be a problem,
since it is auto-detected. (You could try an experiment where you use
nxto=1 in the restrained minimization step. Then you could examine the
file with a text editor. But I don't think this will do any good.)


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Received on Tue Jul 31 2018 - 15:00:03 PDT
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