[switching to BlueObelisk-Discuss from BlueOblelisk-Smiles here]
Geoff, I will look at that. What does "fully validated" mean exactly?
I have the SMARTS business for MMFF94 charges working in Jmol now for
getting the atom types -- obviously not validated! -- and I suspect it will
require a bit of hand-crafting.
Egon, I'm using your CDK interpretation of how to handle MMFF94 bci and
pbci. That looks relatively simple.
Still, I would like to know more details. I'll look at that code, Geoff,
and see what I can see about some of those groups. Thanks.
Others with insight into MMFF94 charge calculation?
Bob
On Thu, Apr 26, 2012 at 8:11 PM, Geoff Hutchison
<ge...@geoffhutchison.net>wrote:
> > Today I decided I wanted Jmol to be able to generate MEP mapped van der
> Waals surfaces, and the way I see to do that is to use the MMFF94
> algorithms. Especially because I should be able to easily validate with
> PubChem, because their structures are delivered with MMFF94 charges.
>
> Open Babel has a fully validated implementation of MMFF94 and charges,
> thanks to Tim Vandermeersch. I think ChemKit also has a full MMFF94
> implementation, although you'd have to ask Kyle if he validated it.
>
> The MMFF94 atom types are quite opaque, and I'm not sure they can all be
> done via SMARTS. Tim hand-coded the aromaticity model and typing in
> src/forcefields/forcefieldmmff94.cpp.
>
> -Geoff
--
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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