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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Neeru Sharma
Project Engineer,
Molecular Modelling Team, Bioinformatics Group,
Centre for Development of Advanced Computing (CDAC),
Ganeshkhind, Pune University Campus,
Pune, Maharashtra - 411007
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 11 2011 - 06:00:07 PST
