Jmol 12.3.24 will calculate charges using the MMFF94 model. Thus, you will
be able to do this:
load caffeine.xyz
calculate partialcharge
isosurface vdw map mep
It was an interesting challenge making this work. Looking over the code for
the CDK and OpenBabel, I'm not at all convinced it is done correctly there.
The task is quite complex, involving assigning very exacting atom types
that push SMARTS matching to the limit (and a little beyond, actually) as
well as doing a full Hueckel aromaticity analysis and, in the end,
identifying atoms that are in the same aromatic ring even. Very tricky to
get right. But it's validated to a standard deviation of 0.0002 over the
17,000 atom/761 model validation set provided by Merck.
Thanks go to Kyle Lutz (and his excellent coding for Chemkit) for sharing
with me his excellent understanding of MMFF94. I couldn't have done it
without his help.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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