[gmx-users] parameters of GppNHp

[Justin Lemkul]

On 9/18/16 3:37 AM, Dd H wrote:
> Hi everyone,
> I want to simulate a protein-ligand complex. The ligand is a GppNHp
> molecule and an analogue of GTP. I cannot find parameters of GppNHp in
> AMBER parameter database (parameters of GTP are supplied there). Can you
> tell me how to get the parameters of GppNHp? Thank you in advance!
>

Derive them in a manner consistent with the parent AMBER force field.  There are 
lots of ways to start going about this, e.g. online servers, GAFF, antechamber, etc.

-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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