[AMBER] Problem with GDP parameters generation

From: neeru sharma <neeru.bioinfo.gmail.com>
Date: Sat, 10 Dec 2011 15:03:44 +0530

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

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 while
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 for
GDP, can anyone provide me the same so that I can compare and see where the
parameters are differing.


Neeru Sharma
Pune (India)
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Received on Sat Dec 10 2011 - 02:00:03 PST
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