Subject: autodock's autogrid3 > empty map files & 2 other small autodock q uestions

From: Matthew Lee <[email-masked]>
Date: Fri, 26 Jul 2002 15:45:43 -0700

Have any of the autodock users ever experienced autogrid3 leading to
spurious affinity maps where every grid point energy in each of the
macro.X.map files is simply the "constant" as defined in the .gpf (except
for the electrostatic potential map, which appears valid)?  I'm puzzled by
this as there are no errors reported.

With one ligand, which is highly rigid (2 rotatable bonds)I can get
autogrid3 to run without any problems.

On the problem ligand, the only difference I can see is that the ligand is
much more flexible.  deftors detects 9 rotatable bonds.  Does anyone have
any ideas on why autogrid3 might not be working properly?  In both the
working and problematic ligands, I am starting with mol2 files that have the
charges defined.

As a side discussion, I have two more questions/concerns.  

1) I noticed that deftors changes C to A for all the "Active" AKA "Core"
carbon atoms, but the 'A' atom type is not discussed at all in the
documenttion.  Any comments on this?

2) When deftors completes, it says:
----------------------
Checking charges in ... using "chckqs";
...
chckqs - Command not found
----------------------

I looked at deftors and it's calling .../autodock/dist305/share/check-qs.
Then I looked at check-qs, which on line 23, is calling for "chckqs", which
doesn't seem to exist *anywhere* in the autodock distribution tree.  There
is a "checkqs", which appears to just be an alternate (antiquated?) version
of check-qs.  Any comments on this?

--Matt Lee

*******************************************************************
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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