Dear Jason,
Thanks for the reply and sorry the late reply. I have pmemd.cuda installed
in ' /home/user1/amber12/bin/ ' and I am running pmemd.cuda from the folder
" /home/anu/ " using the following script
*********************************************************************************************
#!/bin/csh
#PBS -N PDP
#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l walltime=24:00:00
#PBS -e error.log
cd /home/user1/amber12/bin
pmemd.cuda -O -i /home/anu/md.in \
-c /home/anu/eq.rst \
-p /home/anu/PDP.top \
-ref /home/anu/PDP.crd \
-o /home/anu/md.out \
-r /home/anu/md.rst \
-x /home/anu/md.crd \
-inf /home/anu/md.info
********************************************************************************************
I have all input files including angle_pbc.RST file in ' /home/anu/ '
folder. As you said, where should I keep the RST file, in ' /home/user1/
' or in ' /home/user1/amber12/bin/ ' ?
I have also tried with changing file permission to global, still the job
terminated with same error.
Thanks and regards
Anu
On Wed, Nov 20, 2013 at 6:05 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Nov 20, 2013 at 6:26 AM, anu chandra <anu80125.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am trying to use Amber 12 CUDA-PMEMD for an angle restrained MD
> > simulation. Unfortunately, simulation terminated with following error.
> >
> >
> >
> *****************************************************************************
> > Warning: Error opening "Old" file from subroutine OPNMRG
> > File = angle_pbc.RST
> >
> >
> *******************************************************************************
> >
>
> It seems like the angle_pbc.RST file either cannot be found or cannot be
> opened. It would help to know the actual command that you're using to run
> pmemd.cuda. As a note, angle_pbc.RST must be in the same folder that
> you're running pmemd.cuda from, NOT the same folder as the mdin file
> (unless of course the mdin file is in the same folder as you are running
> pmemd.cuda in).
>
> You should also check the permissions (if you can open it in a text editor
> then that should be all the permissions you need).
>
> Good luck,
> Jason
>
> P.S.: I'm assuming all of the tests run correctly, yes?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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>
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Received on Thu Nov 21 2013 - 23:30:03 PST
