[gmx-users] Re: GROMACS-CYSTEINE PROTEASES

[MUSYOKA THOMMAS]

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 <jalemkul at 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.
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>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
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-- 
*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 - thommas at sia.co.ke
*

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