[gmx-users] parameters of GppNHp

[Justin Lemkul]

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" <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
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================