On 9/19/16 11:18 PM, Anu George wrote:
Hi everyone,
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
You'll have to explain better what exactly you did and what didn't work. "It
was not working" is a useless statement in any scientific field. What did you
do? What failed? If it's a problem with some external program/server, you need
to consult its documentation, FAQs, and contact its developer(s) for help. If
it's a GROMACS problem (specific error message, difficulty putting parameters in
the right format, etc) then describe the situation completely.
-Justin
Dading Huang- if you are able to create the topology and coordinate file for
the same please share the details
Thanks in advance
Anu George
----- Original Message -----
From: "Dd H" <ddhe...@gmail.com>
To: gmx-us...@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 <jalem...@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
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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
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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