Subject: hyperchem in tandem with autodock

From: "will" <ewlowe!at!helios.acomp.usf.edu>
Date: Wed, 23 Jun 2004 16:24:20 -0400

I'm a biochemistry grad student who has recently been given the task of
learning basic molecular modeling independently.  I have learned the
basics of hyperchem and autodock, and, having no experience in
computational chemistry, have blindly moved forward and my dockings.  It
was recently suggested to me that although hyperchem can be used to find
docking/binding energies through geometry optimizations, I should just
use it to assign charges to my substrates (which are rather small 10-15
C) and use these substrates for my autodock dockings.  However, I was
under the impression that charges were assigned through autodock without
having to use hyperchem.  Please correct me if I'm wrong.  Also, .hin
files are not compatible with autodock and must somehow be converted to
.pdbq files if this method is indeed useful.  I've found a python script
hin2pdbq.py, but don't know how to use it since I have no real knowledge
of how to use linux/python.  I managed to get autodock up and running on
cygwin with some help from the members of this board (thanks).  Any
input would be greatly appreciated.  On a side note, I'm very interested
in learning how to screen a database of possible substrate/inhibitors
with autodock.  I have no idea if an additional program is needed or
what changes to make.  Thanks a lot for the help in advance.
 
Will
University of south florida
ewlowe!at!helios.acomp.usf.edu