[gmx-users] protonating GLUs

[Justin Lemkul]

On 5/30/16 3:40 PM, Irem Altan wrote:
> Hi,
>
> I am trying to add an extra proton to some of the glutamates in my system. I am using pdb2gmx with the -glu flag. When I tell gmx to add an extra proton, what determines which oxygen atom will be protonated? Is it always attached to OE2, as the aminoacids.hdb file suggests? (I’m using amber03) Is there a way to attach the extra proton to OE1 instead?
>

It's defined by the force field.  Choice of oxygen for protonating should be 
irrelevant; the side chain will rotate over time.

-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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