[gmx-users] small molecule aggregation analysis
jalemkul at vt.edu
Tue May 24 18:35:06 CEST 2016
On 5/24/16 12:19 PM, Surahit Chewle wrote:
> Hello Everyone,
> I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in
> small organic solvent, methanol on Gromacs 4.6.5
> as far as I have read, there are many tools available for protein
> aggregation, but if you can suggest a tool of choice for small molecule
> aggregation, for ex, radial distribution function that will be helpful.
> Fairly new to Gromacs and this is my first post, so kindly be gentle if I
> have made a mistake posting this message.
I don't think there's necessarily any tool that is predisposed to being intended
for protein aggregation; most of the analyses applied in those cases are rather
generic - contacts, distance matrices, buried SASA, possibly RDF, etc.
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
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