Re: [AMBER] Error with angle restrain in CUDA PMEMD

From: Jason Swails <>
Date: Fri, 22 Nov 2013 09:27:11 -0500

On Fri, 2013-11-22 at 12:36 +0530, anu chandra wrote:
> 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

No you are not.

> *********************************************************************************************
> #!/bin/csh
> #PBS -l nodes=1:ppn=4:gpus=1
> #PBS -l walltime=24:00:00
> #PBS -e error.log
> cd /home/user1/amber12/bin

With this command you change to the directory /home/user1/amber12/bin

> pmemd.cuda -O -i /home/anu/ \
> -c /home/anu/eq.rst \
> -p /home/anu/ \
> -ref /home/anu/PDP.crd \
> -o /home/anu/md.out \
> -r /home/anu/md.rst \
> -x /home/anu/md.crd \
> -inf /home/anu/

You are now running pmemd.cuda _inside_ /home/user1/amber12/bin. This
is unusual. In general, you do NOT have to run programs in the same
folder that they are installed in. This is the relevant part of your
input file:


You tell pmemd.cuda that your restraint file is "angle_pbc.RST", so it
tries to open "angle_pbc.RST". Since your current directory
is /home/user1/amber12/bin, it tries to open the
file /home/user1/amber12/bin/angle_pbc.RST -- a file that does not
exist. This file is actually in /home/anu. You can either specify the
full path of angle_pbc.RST inside or go to /home/anu/ and run the
simulation from there. This is the PBS script that I would use [1]:

#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l walltime=24:00:00
#PBS -e error.log

cd /home/anu

pmemd.cuda -O -i \
                -c eq.rst \
                -p \
                -ref PDP.crd \
                -o md.out \
                -r md.rst \
                -x md.crd \


Understanding what happened here and why you got your error should help
you debug problems in the future.

Good luck,

[1] Actually, the first lines of my PBS scripts look something like

#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l walltime=24:00:00
#PBS -e error.log


This command automatically changes to the directory from which you
submitted the script. My Wiki has a helpful page about more advanced
uses of PBS that help make more efficient use of available resources:

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Nov 22 2013 - 06:30:03 PST
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