[gmx-users] MD of two structure together-receptor+ligand

[Justin Lemkul]

On 10/22/15 1:23 PM, Nikhil Maroli wrote:
> Dear Gromacs users,
> i wanted to do MD after docking,i done docking and i selected one
> conformation  i have receptor pdb and ligand pdb and i made one pdb with
> both ?
> now i wanted to do MD and see how the interaction goes on and to
> learn/predict inhibition and antagonist behavior of the system.
> so can anyone tell me how should start ?
> should i start with one single pdb if yes how should i add topolgy for
> drugs?
> i have topolgy parameters from individual system generated from the server
> i hope someone can help out here.

Google knows a lot, too.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-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 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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