elkhot at gmail.com
Mon Nov 9 17:55:24 CET 2015
Thank you for your response.
When writing gmx, it gives the command not found. (Note I use windows)
On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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