AMBER: Complexes

From: Beale, John <>
Date: Tue, 8 May 2007 13:54:34 -0500

I am new to AMBER and I need help with something that I am sure is
relatively simple. I am trying to create complexes of small drug
molecules with proteins. I have used a docking program to create pdb
files of candidate drug-protein complexes. The problem comes in
submitting these to AMBER. When I try to run LeAP on the complex pdb
file it fails because the portion of the pdb file that represents the
ligand doesn't have the right information. Specifically, the ligand in
the pdb file is described by simple atom types without positional
designations. For instance, the part of the pdb file representing the
ligand gives the atoms as HETATM and may use "C" ten times, instead of
"C1, C2, C3, etc.". It is the same with hydrogens, oxygens, and sulfurs.
LeAP complains about this and will not save parameters. Can anyone tell
me how I can "fix" my pdb file to contain a model with unique ligand
atoms that will run through LeAP? I have tried everything that I can
think of, and have never been successful.


I have processed my ligand molecules through antechamber and have prepin
and frcmod files for each. Will this help me?


I am sorry to present such a simplistic problem to this body, but I
don't know how to proceed.


John Beale


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Received on Wed May 09 2007 - 06:07:33 PDT
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