AMBER Archive (2002)

Subject: Save from LEaP to a PDBQ file ?

From: jeff dyason (j.dyason_at_mailbox.gu.edu.au)
Date: Thu Apr 11 2002 - 22:50:32 CDT

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Hi,
        I have set up my protein structure in LEaP and before running any
calculations I want to dock in a ligand using AutoDock. This requires a
modified pdb file be set up which has a partial charge for each atom of
the protein, usually in the B factor column. Is there any way to convert
one of the output file types available from LEaP to the pdbq format. I
have had a quick look at the manual for the programs supplied with AMBER
7 like ptarj and Carnal, as well as OpenBabel but I can't see an obvious
way of obtaining a pdbq file from any files that LEaP writes out.
        I thought that Antechamber may be able to do what I want but when I
try the following the program crashes and dumps core :-

antechamber -i leap.pdb -fi pdb -o leap.pdbq -fo mpdb

leap.pdb is a pdb file output from LEaP and is of a protein around 400
residues and I am assuming the mpdb file format is at least close to
what I want as it appears to be generated from the program delphigen
within the antechamber suite of programs.

Any suggestions appreciated.

Bye Jeff.
-----------
Jeff Dyason e-mail: J.Dyason_at_mailbox.gu.edu.au
Centre for Biomolecular Science and Drug Discovery
Griffith University (Gold Coast Campus)
        http://www.gu.edu.au/centre/cbsdd
PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028
Queensland 9726 Australia Fax: +61 7 5552 8098

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