[gmx-users] evaluation of influence of pH on the stability of protein

[Justin Lemkul]

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

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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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