[gmx-users] parameters of GppNHp

[Anu George]

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

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.