Re: [AMBER] Problem with GDP parameters generation

From: Marc van der Kamp <>
Date: Sat, 10 Dec 2011 11:08:40 +0000

Hi neeru,
You can find parameters/topology (+ reference) at


On Saturday, 10 December 2011, neeru sharma <> wrote:
> Dear amber users,
> 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, the GDP molecule is not
> fitting in the binding pocket of protein (Upon superimposition of the
> generated topology and coordinate file with the initial PDB input file,
> they were not being superimposed).
> Upon tracking the whole process, it was found that the error might be
> using antechamber for generating prepin file using Gaussian output file as
> the input.
> Can anyone please suggest some way to apply some constraints in the
> antechamber command itself. OR if anybody has the paramters or topology
> GDP, can anyone provide me the same so that I can compare and see where
> parameters are differing.
> Thanks
> ----
> Neeru Sharma
> Pune (India)
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Received on Sat Dec 10 2011 - 03:30:02 PST
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