Subject: Re: CCL: hyperchem in tandem with autodock

From: "Tamas E. Gunda" <tgunda<<at>>puma.unideb.hu>
Date: Thu, 24 Jun 2004 09:13:31 +0200

Will,

Try to use Mol2mol for converting hin files to pdbq files
http://web.interware.hu/frenzy/mol2mol

Tamas Gunda
University of Debrecen, Hungary
tgunda *AT* puma.unideb.hu

----- Original Message ----- 
From: will
To: chemistry<<at>>ccl.net
Sent: Wednesday, June 23, 2004 10:24 PM
Subject: CCL:hyperchem in tandem with autodock

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