Re: [Jmol-users] Re : Re: Jmol partial charge calculation

[Robert H. <ha...@st...>]

OK, I've got it.  A good use for -0.0 (which is NOT exactly the same in
Java as 0.0)

On Sat, May 12, 2012 at 10:22 PM, Robert Hanson <ha...@st...> wrote:

> how interesting! Yes, that makes sense. The only way I can think of to fix
> this is to set one of the partial charges to a very small number -- 1E-10
> -- so that it triggers Jmol to consider partial charges as having been set.
> Any objection to that?
>
> Bob
>
> On Fri, May 11, 2012 at 9:47 AM, Pillot Paul <
> pau...@ac...> wrote:
>
>> I've played with this new feature as well and I've found an unexpected
>> behavior : when the molecule is an alkane the VDW surface is not computed
>> and an error is issued, stating that the file does not contain partial
>> charges to display the MEP surface.
>>
>> The calculate partialcharge command runs just fine. Of course there are
>> no partial charges for these alkane models so that is certainly the cause
>> for the error.
>>
>>
>> Nonetheless, in modelkit, if I create first a model with partial charges
>> and a MEP surface, and I subsequently remove from that model atoms or
>> reduce bonds order to get an alkane, then a green MEP surface is displayed.
>>
>>
>> In Otis' page, this problem doesn't appear when one chooses to start from
>> C2H6 (green MEP surface is displayed). I suspect that's because the
>> ethene.txt file used there has charges set (-0.0680 for C and 0.0227 for H)
>>  ... In Bob's "simple" page, this can be tested by loading ethan from NCI
>> and try to display MEP (no surface displayed).
>>
>> Paul
>>
>>
>>
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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
>



-- 
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