yes -- that would fix it. It just wasn't seeing any charges if the MMFF94
charge calculation set them all to 0.
On Mon, Aug 24, 2015 at 1:20 PM, Otis Rothenberger <osrot...@chemagic.com>
wrote:
> Bob,
>
> OK, you’ll probably fuss, but this fixes it:
>
> *{*}.partialcharge=0.01*;select *;calculate partial charge
>
> The calculate charges appear correctly and 0.01 is gone.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
> On Aug 24, 2015, at 1:49 PM, Otis Rothenberger <osrot...@chemagic.com>
> wrote:
>
> Bob,
>
> The script I’m using is old. It predates your adding the charges to the
> extractable molfile. The production version I’m now using does have the
> charges in the extracted molfile, and it does draw the MEP of alkanes. The
> molfile is below. This is an easy work around that may not really be a work
> around. The complete MEP script that I use already assigns partial charges
> to the hydrogen halides because I think MMFF94 does not work with these
> binary compounds.
>
>
> http://chemagic.com/molecules/models/methane.txt
> __Jmol-14_08241513413D 1 1.00000 0.00000 0
> Jmol version 14.2.4_2014.08.03 2014-08-03 08:56 EXTRACT: ({0:4})
> 5 4 0 0 0 0 1 V2000
> 0.00000 0.00000 0.00000 C 0 0 0 0 0 0
> 0.55410 0.79960 0.49650 H 0 0 0 0 0 0
> 0.68330 -0.81340 -0.25360 H 0 0 0 0 0 0
> -0.77820 -0.37350 0.66920 H 0 0 0 0 0 0
> -0.45930 0.38740 -0.91210 H 0 0 0 0 0 0
> 1 2 1 0 0 0
> 1 3 1 0 0 0
> 1 4 1 0 0 0
> 1 5 1 0 0 0
> M END
>
> <JMOL_PARTIAL_CHARGES>
>
> 5
> 1 0.0
> 2 0.0
> 3 0.0
> 4 0.0
> 5 0.0
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
> On Aug 24, 2015, at 1:05 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> I think that's been there forever. HC have 0 partial charge, so it is
> never saved, then its absence is flagged.
>
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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