Re: [AMBER] Need GDP parameters for ff03

From: FyD <>
Date: Sun, 11 Dec 2011 20:24:24 +0100


> 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

regards, Francois

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Received on Sun Dec 11 2011 - 11:30:03 PST
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