[gmx-users] protein-protein interaction

[Mahboobeh Eslami]

Thanks so much for your help 

    On Thursday, January 28, 2016 8:16 PM, Justin Lemkul <jalemkul at vt.edu> 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

-- 
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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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