Thanks so much Justin, I really appreciate your guidance and your input in this forum. Thanks.
On Sun, Aug 25, 2013 at 6:00 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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<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 > > -- > ==============================**==================== > > 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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * "Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can." - John Wesley. * -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
