[gmx-users] evaluation of influence of pH on the stability of protein
jalemkul at vt.edu
Tue Aug 30 14:38:37 CEST 2016
On 8/29/16 3:10 PM, Mahboobeh Eslami wrote:
> Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks
Protonate the protein and any other relevant species in different forms
characteristic of the dominant form at each given pH. The better way to do this
is using constant-pH methods, such as those available in CHARMM. I believe
there are implementations of this in GROMACS, but they are not natively supported.
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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