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
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Received on Sat Dec 10 2011 - 07:00:02 PST
