[gmx-users] interaction energy

Justin Lemkul jalemkul at vt.edu
Sun Mar 30 17:10:23 CEST 2014

On 3/30/14, 10:55 AM, pratibha wrote:
> Hi all,
> I would like to calculate LJ and coulombic interaction energy between
> protein backbone and ligand And also between protein sidechain and ligand. I
> am able to calculate interaction energy between protein and ligand by
> specifying these groups in *.mdp file, creating tpr, using mdrun -rerun
> option and finally using g_energy. But I am unable to understand how to
> dissect this contribution into protein backbone and sidechain?
> If I specify energygrps as Backbone LIG,
> then I am getting following error:
> atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in
> different energy groups
> which I understand (from previous posts) comes when we remove any group
> necessary for other functions (although we dont need these in our energy
> calculations).
> So, then I have specified following energy groups in my *.mdp file:
> Protein Backbone LIG
> But now I am getting following error:
> Atom 1 in multiple Energy Mon. groups (1 and 2)
> My question is how can I calculate protein's backbone and sidechain
> interaction energies with the ligand separately?

Specify them as separate groups.  The backbone is a subset of the whole protein, 
hence the error above.  Moreover, I don't think the "Backbone" group is what 
you'll want - it only contains N, CA, and C atoms, no H or O.  You probably want 
"MainChain+H" to include possible electrostatic/hydrogen bonding interactions, 
then "SideChain" for the remaining sidechain atoms.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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