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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