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--- Neeru On Mon, Dec 12, 2011 at 12:54 AM, FyD <fyd.q4md-forcefieldtools.org> 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. . http://q4md-forcefieldtools.org/REDDB/ (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 > 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/amberReceived on Sun Dec 11 2011 - 20:00:03 PST