[gmx-users] Error in energy groups

[masoud keramati]

tnx Dr.Lemkul

yes the problem was in the tc-grps.
tc-grps        = Protein Non-Protein
and there is no Non-Protein group in index file.
it's true that i use System for tc-grps?

On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/24/16 3:17 PM, masoud keramati wrote:
>
>> Hi all
>>
>> i have a protein with six chain.
>> i create an index file that include each chain (chA chB ..)
>> in mdp file i define energy groups such that:
>> energygrps   = chA chD
>>
>> for grompp i used this command:
>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr
>>
>> but i got this error:
>> "Group Non-Protein referenced in the .mdp file was not found in the index
>> file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp "
>>
>> what's wrong with this?!
>>
>>
> You have some setting that uses Non-Protein but you haven't got that in
> your index file.  Check tc-grps as the most likely culprit.  If your index
> file *only* contains the chains that you've specified, then you're going to
> encounter problems.  In general, add groups that you need and leave the
> default groups (System, Protein, Non-Protein, etc.) in place for ease of
> use.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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