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: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
> 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
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Received on Mon Dec 12 2011 - 06:00:05 PST
