[gmx-users] parameters of GppNHp

Fri Sep 30 12:13:48 CEST 2016

Hi,
You should add "-nc" option to your antechamber command, which specifies
the net charge of your unit. You can type "antechamber -h" command to get
more information.

On 30 September 2016 at 16:47, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You'll probably have better luck getting help with how to use AmberTools
> from the AmberTools documentation and the Amber mailing list. And search
> Google for that error message first, because it's probably been seen
> before.
>
> Mark
>
> On Fri, Sep 30, 2016 at 10:44 AM Anu George <g_anu at blr.amrita.edu> wrote:
>
> > 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
> > >>>
> > >>> ==================================================
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
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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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