From owner-chemistry@ccl.net Tue Sep 20 07:29:54 2005
From: "CCL" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: using pdb2pqr on a non-standard, non-parametrized residue
Message-Id: <-29240-050920065020-20319-MxPps1ulpfG46D/+2PQnqg]=[server.ccl.net>
X-Original-From: Dr Seth Olsen <s.olsen1]=[uq.edu.au>
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Date: Tue, 20 Sep 2005 20:50:07 +1000
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Sent to CCL by: Dr Seth Olsen [s.olsen1]=[uq.edu.au]

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Hi CCLers,

I must generate likely protonation states for a protein containing a
non-standard residue, and I have decided to use PDB2PQR to perform the
protonation and determine titratable pKa's.  Of course, however, PDB2PQR
chokes on the non-standard, non-parametrized residue.  In order to
generate the full PQR I must determine charges and radii for all atoms
of the non-standard residue.  It would seem that the best way to
generate the charges is to feed a model of the residue through the RESP
charge generation algorithm.  However, I was wondering what is the best
way to determine the radii?  Is there an available software package that
will do this?  

Cheers,

Seth

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Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1]=[uq.edu.au
Web: www.ccms.uq.edu.au 

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