[gmx-users] Error in energy groups

[Justin Lemkul]

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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