Re: AMBER: Complexes

From: M. L. Dodson <>
Date: Tue, 08 May 2007 14:14:59 -0500

Beale, John wrote:
> 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

I don't know of any off the shelf s/w that will do the job, however:
since you have prepin files, you know the names AMBER assumes the atoms
to have. So I would proceed from that information to a custom perl
script to do the renaming. You can verify the correspondence of atom
number to name by looking at the ligand pdb file in one molecular viewer
(that allows mouse atom selection) and the prepin (or a pdb file derived
from it) in another viewer window. From that, create a perl hash
mapping the atom NUMBER in the ligand file you want to edit to the
correct atom NAME (from the prepin file). Running this over the ligand
pdb file should fix it just fine.

You can do the same with awk rather than perl if you know awk better.

You might be able to do it with a LEaP alias table corresponding to the
perl hash described above, but I have less experience with that. In
analogy to the hammer and nail saying, to perl hackers, all problems
look like perl hashes.

If you want to avoid this (possibly reusable for similar problems)
programming, you can achieve the same thing with an ordinary text editor.

Bud Dodson
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-56_three-386_one
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Received on Wed May 09 2007 - 06:07:33 PDT
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