[gmx-users] MD at different pH

Anu George g_anu at blr.amrita.edu
Wed May 3 16:30:50 CEST 2017

Thanks Justin for the information.
But I had a further question regarding the simulation-if the active monomer exists only in the acidic pH, then will carrying out a simulation of the monomer with a drug  at neutral pH help?
Anu George

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, May 3, 2017 5:37:33 PM
Subject: Re: [gmx-users] MD at different pH

On 5/2/17 11:31 PM, Anu George wrote:
> Dear Gromacs users,
> I am working on a tetramer(human beta-2 tryptase) protein which exist as an active monomer at an acidic pH of about 6..If I have to do a molecular dynamic simulation of the monomer with a small molecule,  should the simulation be carried out  at this pH ? what are the steps I should follow?

Calculate the pKa values for titratable residues and select their dominant 
protonation states at that pH when running pdb2gmx.



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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