Re: [AMBER] Problem with GDP parameters generation

From: neeru sharma <>
Date: Mon, 12 Dec 2011 20:44:44 +0530

Thanks David for these suggestions. Actually, I am new to amber and hence
might have missed these things. Now I will definitely look into it.


On Mon, Dec 12, 2011 at 7:22 PM, David A Case <>wrote:
> On Sat, Dec 10, 2011, neeru sharma wrote:
> > Actually, I tried to superimpose the topology and coordinate files
> > (generated using amber) over my input PDB structure of GDP but they were
> > not showing any superimposition.
> As I (tried to) say earlier: this is not necessarily an indication that
> anything is wrong.  It's not clear how this happened, though, since we
> don't
> know any of the commands you used to generate the parameters.
> >
> > Another amber mailing list member Marc has suggested to use the GDP
> > parameters given at:
> > But these are in AMBER94 forcefield and I would be using AMBER03 for my
> > simulation. So, can I use these parameters for AMBERff03 too or some
> > changes are required?
> Opinions differ here.  In principle, you might want to use the same charge
> derivation method for your "ff03-GDP" parameters as was used in generating
> the charges for the protein part of ff03.  Such a consistency sounds good,
> but doesn't really provide any evidence that the interactions between GDP
> and
> water/protein parts of your system are actually correct: first, the
> deficiencies in the charge distribution using the ff03 procedure might be
> different for phosphates than for other types of protein functional groups;
> second, the way in which LJ parameters are derived doesn't easily carry
> over
> to phosphates.
> If you know particular interactions involving the GDP that are important to
> you, you might use the published GDP parameters with both ff94 and ff03 and
> see how much they differ.
> ....dac
> _______________________________________________
> 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 Mon Dec 12 2011 - 07:30:02 PST
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