Subject: CCL: (more information) local search in AutoDock

From: Robert Flight <l72k6{at}unb.ca>
Date: Wed, 25 Jun 2003 10:52:47 -0300

Just to clear up some misunderstandings from my first post:

I have been using AutoDock 3.05 and ADT for almost a year now, performing
GA-LS runs for many different ligands and receptors, always using random start
coordinates for the ligand.  I know that a lot can go wrong with the docking
box and ligand coordinates.  What I am trying to do is use just a local search
to minimize the coordinates of a ligand pose from a GA-LS run.  I've double
checked the coordinates, and in the DPF it says the ligand center is very
close to the center of my docking box.  My docking box is the same one I have
used for the past year for docking, and is the same one that produced the pose
I want to minimize.

> From the DPF:
ligand center - 2.515 64.475 68.117
Grid box center - 3.524 64.788 64.837

And I still get the problem I outlined below.  From what I can tell, there is
no reason for the ligand to end up outside the docking box.

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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