Subject: solution to empty affinity maps by autodock's autogrid

From: Matthew Lee <[email-masked]>
Date: Mon, 29 Jul 2002 10:09:00 -0700

I have found the solution to my problem with Autodock 3.0's
autogrid3.  As reported earlier, autogrid3 was creating grid map files with
all zero's (or whatever "constant" was defined to in the GPF file).

	Again, with one ligand, everything works fine, but in another ligand
that happened to be much more flexible, I was having autogrid3 problems.
The extra flexibility was unrelated to the problem.

	The problem lies in the "gridcenter" line of the GPF file.  I used
(as recommended by the manual) mkgpf3 to create the GPF file, but this
mkgpf3 script defines the center of the grid based on the ligand's
coordinates, not based on the protein's (the manual does not say it's doing
this).  Perhaps this is a feature in some instances?!?!  

	In my problem case, the center of mass of the protein was about 60
Angstroms away from that of the ligand.  Thus, wsing the GPF file created by
mkgpf3 caused autogrid3 to produce useless affinity map files, presumably,
because the protein was completely outside of the grid.  Naturally, the
affinities to every point in the grid would have been zero (or whatever you
defined constant to be) if the protein is nowhere to be found in the grid.
The most frustrating part of this was that there were no warning or error
messages.  In fact, the final message reported "autogrid3: Successful
Completion."  But of course, using these atom affinity maps leads to
unsuccessful docking with autodock3.

	The solution is to edit the GPF file created by mkgpf3, using
"gridcenter auto" instead of "gridcenter x.xx y.yy z.zz".  The auto option,
as documented, uses the macromolecule's center of mass as the grid center.

--Matt Lee

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Matthew Randolph Lee, Ph.D.

Computational Scientist		phone:  (858)410-6534
Lion Bioscience Inc.		fax:    (858)410-6665
9880 Campus Point Drive	      e-mail:  [email-masked]
San Diego, CA  92121
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