Re: [AMBER] Need GDP parameters for ff03

From: neeru sharma <neeru.bioinfo.gmail.com>
Date: Sun, 11 Dec 2011 22:09:50 +0530

Thanks Jason.
Actually, I too have gone through this database for GDP parameters, but
they were in Amber94 ff and I am planning to run my simulations using ff03
forcefield. That is why I am searching for GDP parameters in ff03.

Infact, I tried to generate GDP parameters using antechamber. But the
topology and coordinate files it generated were not in agreement with the
input PDB file for GDP and that is why I am looking for GDP parameters,if
somebody already have them, so that I can compare them with mine.

Thanks

----
Neeru
On Sun, Dec 11, 2011 at 8:09 PM, Jason Swails <jason.swails.gmail.com>wrote:
> The Bryce database is a good place to find such parameters.  See
> http://www.pharmacy.manchester.ac.uk/bryce/amber#cof for GDP parameters.
> However, take care of Carlos' note -- you don't want to mix force fields
> with different charge models.  I think those parameters are predominantly
> compatible with the standard line of Amber force fields (like ff99SB, not
> ff03).
>
> You should check the references to be sure.
>
> HTH,
> Jason
>
> On Sun, Dec 11, 2011 at 8:47 AM, neeru sharma <neeru.bioinfo.gmail.com
> >wrote:
>
> > Carlos,
> >
> > Thanks for your response. I will definitely consider your suggestion
> before
> > performing simulation.
> >
> > Neeru
> >
> > On Sun, Dec 11, 2011 at 7:13 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > there are few parameter sets with the same charge model as used in
> ff03.
> > > The ff99SB protein force field uses the same charge model as ff94
> > (Cornell
> > > et al) and is therefore likely to be compatible with a much broader set
> > of
> > > parameters for small molecules. ff99SB has also been shown in many
> > > publications to perform better for proteins than does ff03.
> > >
> > > be careful that you don't mix different charge models unless you are
> very
> > > sure of what you are doing.
> > >
> > > On Sun, Dec 11, 2011 at 8:35 AM, neeru sharma <neeru.bioinfo.gmail.com
> > > >wrote:
> > >
> > > > Dear AMBER users,
> > > >
> > > > I have to perform MD simulation on a protein-GDP complex and for
> that I
> > > > need GDP parameters for Amber ff03 forcefield.
> > > > Does anyone know where can I get these parameters?
> > > >
> > > > Thanks
> > > >
> > > > Neeru Sharma
> > > > Pune (India)
> > > > _______________________________________________
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> >
> >
> >
> > --
> > Regards,
> >
> > Neeru Sharma
> > Project Engineer,
> > Molecular Modelling Team, Bioinformatics Group,
> > Centre for Development of Advanced Computing (CDAC),
> > Ganeshkhind, Pune University Campus,
> > Pune, Maharashtra - 411007
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
-- 
Regards,
Neeru Sharma
Project Engineer,
Molecular Modelling Team, Bioinformatics Group,
Centre for Development of Advanced Computing (CDAC),
Ganeshkhind, Pune University Campus,
Pune, Maharashtra - 411007
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Received on Sun Dec 11 2011 - 09:00:03 PST