Subject: CCL: local search in AutoDock

From: Robert Flight <l72k6*at*unb.ca>
Date: Tue, 24 Jun 2003 10:07:23 -0300

Hi,

I'm trying to use a local search (pseudo-sw) to minimize a docked pose of a
ligand into a receptor.  When I look at the ligand and the receptor in ADT,
the ligand is in the correct starting position.  The Grid box is large enough
to contain the search space.  I'm using a non-random start, non-random
relative dihedral offset, and initial relative dihedrals, which should all
start the local search from the specified initial coordinates.

The output ligand poses end up completely outside the docking box, and outside
the receptor as well, with an RMSD of 85 Angstroms!!!  Can anyone tell me what
is happening, as I see no reason why the ligand should end up outside the
docking box!

Thank you for your help,

-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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