Re: [Jmol-users] yippee--charges

[Frieda R. <fri...@ma...>]

Congratulations, Bob! what a wonderful addition!
Frieda

On May 7, 2012, at 6:52 PM, Robert Hanson wrote:

> 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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