Rick,
Bob is correct. We looked into this when we put our virtual model kit together.
For more, see the Coulombic interactions section of the following page:
http://towhee.sourceforge.net/forcefields/uff.html
I'm not sure about the user context of what you are suggesting, but we were
hoping to do something similar in 2009. We finally settled on a work around
approach. The model in a Jmol window can query PubChem for the same compound.
PubChem returns an SDF with partial charges. The rendered model will display a
MEP surface. At the time, Bob was kind enough to include a Jmol read of these
PubChem partial charges. There is one caveat. PubChem archived partial charges
assign a value of zero to most alkane C-H atoms. This is not so for cases where
this would clearly not be a decent approximation - e.g. pentane-2-one. Even
with this limitation, Jmol renders a decent MEP for most simple models. I
should also mention that not all PubChem files have partial charges.
We're still looking for an alternative, but we haven't found it yet.
Otis
--
Otis Rothenberger
[email protected]
http://chemagic.com
On Nov 30, 2011, at 1:41 PM, Robert Hanson wrote:
> I don't think the UFF calculation uses partial charges -- or if it does, they
> are already there. It certainly does not generate its own.
>
> On Wed, Nov 30, 2011 at 11:34 AM, Spinney, Richard
> <[email protected]> wrote:
> Is it possible to assign partial atomic charges used in the UFF minimization
> so I can generate a MEP surface? If so how do I assign the charges to the
> atoms?
>
> Thanks, Rick
>
> --------------------------------------
> Dr. Richard Spinney
> The Ohio State University
> Department of Chemistry
> 144 Celeste Laboratory
> 120 West 18th Ave
> Columbus, Ohio 43210
>
> email: [email protected]
>
> Phone: (614) 247 - 6847
> Fax: (614) 292 - 1685
>
>
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>
> --
> 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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> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
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contains a definitive record of customers, application performance,
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