[gmx-users] parameters of GppNHp
g_anu at blr.amrita.edu
Tue Sep 20 05:47:43 CEST 2016
I am also working on simulation a protein-protein complex which has the ligand GppNHp molecule and an analogue of GTP.
I tried to build the topology using GAFF and antechamber. but it was not working.
Please provide the details for obtaining the same
Dading Huang- if you are able to create the topology and coordinate file for the same please share the details
Thanks in advance
----- Original Message -----
From: "Dd H" <ddhecnu at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, September 19, 2016 6:59:01 AM
Subject: Re: [gmx-users] parameters of GppNHp
Thank you. I have found a tutorial and I will try to derive them.
On 19 September 2016 at 00:40, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 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
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