jalemkul at vt.edu
Mon Nov 9 14:31:52 CET 2015
On 11/9/15 5:23 AM, Said wrote:
> I have a gateway access to uppmax. I could have copied 1aki.pdb to my
> account using box.com since scp does not work.
> when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
> it gives me an error with exit code: 225.
There is not point trying to run pdb2gmx with mpirun; preparation steps should
usually be done interactively, ideally on a local machine, and the .tpr file
sent to the cluster to execute mdrun. Most preparation programs need some kind
of interactive input, which can be scripted but it is not always obvious what
needs to be done ahead of time, especially something as complex as pdb2gmx.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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