Thanks so much for your help
On Thursday, January 28, 2016 8:16 PM, Justin Lemkul <[email protected]>
wrote:
On 1/28/16 10:58 AM, Mahboobeh Eslami wrote:
> hi all I have used the HEX software for docking two protein.I want to do
>molecular dynamics simulations on the obtained complex from docking process.
>should the simulation of protein-protein complex be done like the
>protein-ligand complex or the protein in water simulation? How is simulated
>protein-protein complex?
It is no different than simulating a single protein. pdb2gmx will give you
topologies for each chain, then proceed with solvation, etc. like anything else.
-Justin
--
==================================================
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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