[gmx-users] Simulation in Constant pH simulation ...

[Justin Lemkul]

On 6/15/16 11:34 AM, Nikhil Maroli wrote:
> Hi,
>
> I saw that already.
> in yasara software, they  assign the protonation states of amino acids and
> ligands depending on the chosen pH.i know that that classical MD does not
> include dissociation and reassociation of protons, so residues will not
> change their protonation states during the MD.
>
> possibility in gromacs ?
>

You can change protonation states using pdb2gmx.  See the help information on 
how to do it, or the previous threads on this same topic (there are many, even 
recently).

-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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