Re: [AMBER] Problem with GDP parameters generation

From: neeru sharma <>
Date: Sat, 10 Dec 2011 20:21:48 +0530

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. But the input file which I used for
antechamber (i.e. Gaussian output file) was superimposing completely on the
GDP's PDB and dat is why I assume that the problem might be with
antechamber or may be I am missing some constraints or options there.
I am new to amber as well as antechamber, hence I am confused about the
where the problem is lying.

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?


On Sat, Dec 10, 2011 at 8:03 PM, case <> wrote:

> On Sat, Dec 10, 2011, neeru sharma wrote:
> >
> > I have to simulate a protein-GDP complex. For this,I have generated Amber
> > topology and coordinate files for GDP molecule after preparing GDP.lib
> and
> > frcmod.GDP.
> >
> > But the topology and co-ordinates file are quite different from the input
> > PDB file and hence the parameters are also faulty,
> I'm not following you here. How do you know that the parameters (charges,
> bond lengths, etc.) are faulty? The antechamber/GAFF procedure provides
> parameters that are assumed to be independent of the conformation of the
> GDP. Of course, this is an approximation, sometimes a severe one. If you
> want to have more control over which conformations are used in the charge
> fitting part, consider R.E.D.
> [As an aside, my personal view is that there are problems with current
> phosphate parameterizations that go beyond the problem that the charges
> might
> depend upon conformation. We are finishing up a paper on this subject.]
> ...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
AMBER mailing list
Received on Sat Dec 10 2011 - 07:00:03 PST
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