[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

Justin Lemkul jalemkul at vt.edu
Thu Aug 1 22:57:51 CEST 2013

On 8/1/13 4:55 PM, Collins Nganou wrote:
> Dear Justin,
> Thanks....
> I am simulating a DNA with different residues. I am looking the way to
> extract only the energy of adjacent DT. I intend print out this energy
> group via the energygrps = DT
> I would like to have only DT in the index file. But it doesn't work.
> This is the error encounter:
> Fatal error:
> Group DNA 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.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

There are other groups required for proper functioning of your .mdp file.  As 
such, you cannot use an index file with only DT defined.  Just add the DT group 
as a new group into an index file that includes all other necessary groups.



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 at outerbanks.umaryland.edu | (410) 706-7441


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