Re: [AMBER] Need GDP parameters for ff03

From: neeru sharma <>
Date: Mon, 12 Dec 2011 09:07:32 +0530

Thanks Francois for your help. I was searching for the parameters since
last week. I actually need these GDP parameters asap because I have to
start my simulations on urgent basis. Rest all is already ready with me. I
would be thankful if you can now provide the GDP parameters, in whatever
way suitable to you. For rest of the parameters, I can wait till the
release of the database.

On Mon, Dec 12, 2011 at 12:54 AM, FyD <> wrote:
> Neeru,
> > 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?
> We have generated FF libraries for more than 200 cofactors in a single
> and highly homogeneous force field topology database (FFTopDB). Among
> them are GMP, GDP, GTP (or XYP, X = A C G T U; Y = positive integer).
> This work has been done... 2 years ago or may-be even before and was
> never released in R.E.DD.B. simply by lack of time. We are now in the
> process of releasing these data. We have in fact two FFTopDB one
> compatible with the Cornell et al. force field (& the successive
> adaptations: Cheatham et al., Kollman et al., Wang et al. etc...) and
> the other one compatible with the Duan et al. FF (i.e. ff03). We are
> also preparing a version with extra-points.
> I can propose you to wait for the release of the FF libraries in
> R.E.DD.B. . (this coming week)
> in R.E.DD.B.; or I can send you hidden links to download the data you
> need.
> regards, Francois
> _______________________________________________
> AMBER mailing list
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 - 20:00:03 PST
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