Subject: Re: CCL:advice requested regarding overlay software

From: "Tamas E. Gunda" <tgunda_at_puma.unideb.hu>
Date: Fri, 1 Oct 2004 09:31:02 +0200

You may try the fitting with Mol2Mol. It has options to include or not H atoms, to use
different weight factors, to use a list of the atoms to be included in the fitting
procedure (when the molecules are not identical). Batch calculations from multiple
molecule files and output/conversion to a new file of the fitted, superimposed molecules
are also possible. The rms deviations are also calculated.

http://web.interware.hu/frenzy/mol2mol

Hope this helps

Dr. Tamas E. Gunda
University of Debrecen
Medical and Health Science Center
Dept. of Pharmaceutical Chemistry
Debrecen, Hungary
e-mail: tgunda*AT*puma.unideb.hu

----- Original Message ----- 
From: <khunter_at_mta.ca>
To: <CHEMISTRY_at_ccl.net>
Sent: Wednesday, September 29, 2004 3:01 PM
Subject: CCL:advice requested regarding overlay software

> Enzyme crystal structures lack hydrogens and usually contain inhibitors.  Due
> to the size of the crystal structures computing at a high level of theory with
> different substrates is not feasible.  It is our hope to be able to compute
> fragments of the active site at high level of theory and combine them to a
> realistic model.  Is there a program which allows overlaying computed
> geometries and experimental crystal structures using least squares fitting?
> Any advice on how to compare computed with experimental to ensure maximum
> overlap of the combined optimized fragments to the entire crystal.  Is there a
> way to ensure the orientation of the fragments as they would be in the crystal?
>
> Any advice would be greatly appreciated.
>
> Ken Hunter
> Mount Allison University
>
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