[gmx-users] Re: Concerning a Fatal Error!

Arman Mahboubi Soufiani armansoufiani at gmail.com
Mon Oct 15 15:49:19 CEST 2012


Dear Justin,

Thank you for your help, however, the problem was originated from absence
of -table table_d1.xvg flag in my mdrun command.
Now it is fixed.

BR

Arman

On Sat, Oct 13, 2012 at 10:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote:
>
>> Dear Justin,
>>
>> The followings are the two successive commands I used:
>>
>> *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o
>> justPLA-em.tpr
>>
>> mdrun -deffnm justPLa-em*
>>
>>
> These commands would not produce the error posted previously.  The error
> would have resulted from:
>
> mdrun -deffnm justPLA-em.tpr
>
> The fact that the capitalization is different and the nature of the suffix
> supports this conclusion.  It is better to copy directly from the terminal
> rather than try to recreate what you did.  In any case, proper invocation
> of the command should solve the issue.  mdrun is looking for an .xvg file
> containing parameters for a tabulated dihedral; it needs to be named
> appropriately to function correctly.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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