[gmx-users] Determining interactions in Protein-Ligand complex simulations

[Justin Lemkul]

On 4/14/14, 10:03 AM, MUSYOKA THOMMAS wrote:
> Dear users,
> I am doing a 10 ns protein-ligand simulation and would like to determine
> the hydrogen and hydrophobic interactions per each ns and the participating
> amino acid residues.
>
> How do I go about this?
>

g_hbond and g_mindist, combined with suitable index groups.  There are various 
options to use; see the manual.

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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