Subject: RE: electrostatic potential surface

From: "Shobe, Dave" <[email-masked]>
Date: Tue, 16 Jan 2001 10:42:05 -0500

I'd be interested in the anwers to this but I also have a question.
Reducing the molecule, either by adding an electron or by adding hydrogen,
will cause the surface of the molecule (as defined by an
iso-electron-density surface) to move.  How does one normally handle that?

--David Shobe

-----Original Message-----
From: Knut Teigen [mailto:[email-masked]]
Sent: Tuesday, January 16, 2001 7:00 AM
To: [email-masked]
Subject: CCL:electrostatic potential surface

Dear Computational Chemists,

I have a question regarding electrostatic potential surfaces that I hope 
you will be able to help me with:

I have a 30 atom structure of a organic compound.
I would like to calculate the difference in in the electrostatic surface 
potential of this structure and the reduced form of the same coumpound. 
Then I would like to visualize the difference in electrostatic surface 
potential between these two compounds as a colored surface on one of them.

Is there any software available out there that can do this for me?

Kind regards
Knut Teigen
_____________________________________________________

Knut Teigen                                telephone: +4755586328
Dept. of Biochemistry                  fax: +4755586400
Faculty of Medicine                     mobile: +4792428369
University of Bergen                    eMail: [email-masked]
Norway
_____________________________________________________

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From: Richard Gillilan <[email-masked]>
Date: Tue, 16 Jan 2001 13:52:00 -0500

> iso-electron-density surface) to move.  How does one normally handle that?

For proteins, many people use a molecular surface and map the
potential (or difference potentials) to it using interpolation. You do need
to pick one surface or the other if there is a structural difference. You could
even calculate the potential on the surface in the first place, but this is
more difficult. Using empirical FF methods, I did this recently using OpenDX
to compare a couple similar proteins and successfully predict which
sidechains to mutate to functionally convert one to the other:
The experimental work is due to appear in J. Mol. Bio. shortly:

"Localization of the RAR Interaction Domain of Cellular Retinoic Acid Binding Protein-II"
Anuradha Budhu, Richard Gillilan and Noa Noy  (sorry, don't know the issue yet).

 A slightly earlier conference proceeding with more details on the computations and graphics is
still available online: http://w3.pppl.gov/vde2000/eproceedings.html
"What's Different in These Two Pictures? Structural Biology Using OpenDX", R. Gillilan

Another interesting approach would be to actually do isosurfaces of the
potential difference. This could be done quite easily with OpenDX and
probably a number of other progams (perhaps Grasp). I think the result
will be a bit more difficult to understand and visualize.

Richard Gillilan
MacCHESS
Cornell University