Modeling apps. for the classroom?

Bernard P. Murray, PhD bpmurray*STUFFER* at socrates.ucsf.edu
Thu Oct 8 15:34:14 EST 1998


In article <361c5e99$1$xnlawnl$mr2ice at news.igalaxy.net>,
kayspamjay at igalaxy.net wrote:

> Hello,
> 
> 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.  

I'm not sure if this is what you want but I start with 3 D
coordinates for the small molecule, either from structures
grabbed from the net or those generated "de novo" using
the CORINA facility on the Gasteiger page;

http://www2.ccc.uni-erlangen.de/services/3d.html

To do this you have to be able to write your molecule in
SMILES format but this is quite fun to learn and use.

I then use MOPAC 6.0 to optimise the structure and to generate
the partial charges.  I actually use the version for DOS
(compiled under the DJGPP environment) but there are Linux
versions out there.  I have some AWK scripts for interconverting
file formats (Babel wasn't quite enough).
     This may seem like a trip around the houses but the price
is perfect and the minimisation can be run on a cheapo PC.
There is a wide variety of programs for visualising MOPAC
generated structures.
     I hope that this helps,
          Bernard
-- 
Bernard P. Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA



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