Hi,
This error is similar to your previous error. How did you fix the
previous error ?
Some general advice on your batch script,
insert some debugging commands. For example after cd $TMPDIR
and after each pmemd command:
pwd
ls -l
In that way, you can determine which files are missing and what
needs to be corrected.
FWIW, note i can't see color when i read your emails.
scott
On Mon, Aug 06, 2018 at 09:38:36PM +0000, Debarati DasGupta wrote:
> I have a protein to run minimization.
> I created the solvated prmtop inpcrd files using tleap.
> but inspite of running minimization 10 times I get the same error
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> getting new box info from bottom of inpcrd
>
> Error opening unit 30: File "Dimer.crd" is missing or unreadable
> 56,3 Bot
On Tue, Jul 31, 2018 at 09:51:56PM +0000, Debarati DasGupta wrote:
> 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'
> cd $PBS_O_WORKDIR
> cp leap.in $TMPDIR #copies files to home directory
> cp t.pdb $TMPDIR
>
> cp *.in $TMPDIR
> cp Protein.* $TMPDIR
> cd $TMPDIR
> #module load intel/15.0.3
> #module load mvapich2/2.1
> module load amber
> module load cuda
> #tleap -f leap.in
> #cp *.pdb *.top *.crd $PBS_O_WORKDIR #copies output results back to home directory
>
> pmemd.cuda -O -i min_restrained.in -o min_restrain.out -c Protein.crd -p Protein.top -r min_restrain.rst -ref Protein.crd
>
> pmemd.cuda -O -i min.in -o min.out -c output.rst -p Protein.top -r min.rst
>
> pmemd.cuda -O -i heat.in -o heat.out -c min_restrain.rst -p Protein.top -r heat.rst -x heat.mdcrd -ref min_restrain.rst
>
> pmemd.cuda -O -i prod.in -o prod.out -c heat.rst -p Protein.top -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 <david.case.rutgers.edu>
> 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.)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 06 2018 - 17:00:03 PDT
