Justin Lemkul jalemkul at vt.edu
Sun Aug 25 18:00:34 CEST 2013

On 8/25/13 11:35 AM, MUSYOKA THOMMAS wrote:
> Hello,
> I am trying to minimize my ligand-protein structures but when I run the
> code,
>   mdrun -v deffnm em.tpr
> i am getting the error:
> Program mdrun, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/gmxfio.c, line: 519
> Can not open file:
> topol.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>   Any one with any solution to get through this.

Your command is incorrect for two reasons.

1. The option (like all Gromacs options) needs to be preceded by a hyphen, i.e. 
-deffnm, not deffnm.  mdrun is the only Gromacs tool that does not check the 
validity of the options passed to it.  Thus, "deffnm em.tpr" is completely 
ignored and mdrun falls back on its default file name for -s, topol.tpr, which 
does not exist.

2. Had you used -deffnm, mdrun would have also failed, because it would go 
looking for a file named "em.tpr.tpr."  The string passed to -deffnm is just the 
prefix of the files, because it is applied to all files (input and output).

Thus, the correct command is:

mdrun -v -deffnm em



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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