[gmx-users] pdb2gmx and the Glu residue

[Justin Lemkul]

On 4/25/15 10:40 AM, Brett wrote:
> Dear All,
>
> In the top file produced by H++ server for AMBER, if there is no charge for the Glu, the residue name will be modified to GLH. In our gromacs, we never treat Glu as without charge, thus we do not have GLH residue, am I right?
>

No.  You can treat glutamate however you like (and in this case, it sounds like 
it should be protonated).  Different force fields call the residue different 
things.  It's GLH in AMBER force fields, GLUH in GROMOS and OPLS-AA, and GLUP in 
CHARMM.  Thus, all the force fields support the protonated form.

-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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