Subject: Oxygen in AutoDock.....

From: Robert Flight <l72k6{at}unb.ca>
Date: Mon, 28 Jul 2003 11:09:03 -0300

Hi All,

I have a question about oxygen atoms in the receptor when docking with
AutoDock.  I recently read that Autodock only allows oxygen to be a
hydrogen-bond acceptor if it is bonded to a carbon atom, and it is not
considerd an H-bond acceptor when bonded to two hydrogens (as in water
molecules considered as part of the receptor).  The statement was in regards
to Autodock 2.2, and I am presently using Autodock 3.05.  I'm wondering if
anyone knows if that is still true, and I therefore would need to include a
new atom type to have water oxygens considered as H-bond acceptors.

Any help on this issue is greatly appreciated.

Thank you,

Robert

********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: robert.flight{at}unb.ca
 
********************************

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