Modeling apps. for the classroom?

kayspamjay at kayspamjay at
Thu Oct 8 01:39:07 EST 1998


I am interested in bringing modeling into my general and (survey) organic
classes, and need some advice.  My foremost goal is simply generating an
electrostatic potential surface for something like NAD+ which can then be
used in conjunction with an enzyme's NAD+ binding site as a demonstration of
intermolecular interactions.  I hope to scale this into individualized
student projects.  

I am very uncertain about what programs are most suitable for this small
molecule goal.  I would like to obtain output files which are most likely
usable by a variety of visualization/manipulation apps (eg.
SPOCK/RasMol/etc.) in conjunction with PDB's, etc.  

While I can certainly understand the kinds of things which are involved in
generating an overall electronic picture of a molecule, I can't begin to
guess what parameters might be appropriately used, discarded, or changed for
a given system.  My training was not in this area!  Yet a combination such
as Molden/Gamess seems possible, if I had a set of default parameters which
would work reasonably well for most molecules until I get my feet on the

Is this a workable idea??

We have little money available, so a commercial solution
(HyperChem/Spartan?) is less desirable.  What $$ exists is going towards
some well-powered PC's running Linux (or our institutional NT, if no other
choice is there).  Do these programs generate proprietary output formats if
no other solution exists?

I am sorry for the length of this note, but do appreciate any input from

Dr. Kenward Vaughan
Professor of Chemistry
Bakersfield College
kvaughan at (work)
kaynjay at

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