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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
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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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Dec 11 2011 - 07:00:02 PST
