[gmx-users] parameters of GppNHp

[Anu George]

Hi everyone,
I am trying to do a simulation of "RAS G12V - PI 3-KINASE GAMMA COMPLEX" which has the ligands 'GNP' and Mg2+. For GNP i tried to create the topology by using antechamber giving input as GNP.pdb which was extracted from the pdb file (1he8.pdb) but it is giving the error as 
Error: cannot run "/home/anugeorge/amber16/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" when I run the command 
antechamber -i GNP.pdb -fi pdb -fo ac -o GNP.ac -c bcc -s 2 -ek  grms_tol=0.005

Please suggest a way to overcome this error" 
Thanks in advance
Anu George

----- Original Message -----
From: "Dd H" <ddhecnu at gmail.com>
To: gmx-users at gromacs.org
Sent: Wednesday, September 21, 2016 6:12:54 PM
Subject: Re: [gmx-users] parameters of GppNHp

Hi Anu,
Not very sure what is your trouble. I can figure out two ways to get the
GppNHp parameters:
1). Since GppNHp is very similar to GTP. We can borrow the most of
parameters from GTP (you can find GTP parameters in AMBER parameter
database), then derive the rest missing parameters or borrow them from GAFF
(I don't know whether it's right to mix them up in a molecule).
2). Using GAFF entirely.

Best regards,
Dading

On 20 September 2016 at 23:54, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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