Sure enough. We're just using orbital energies for assigning HOMO in this
case, and there was a bug there. Probably should be using the information
in the file, but we just aren't at this time. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob
On Tue, Nov 15, 2011 at 4:19 AM, Jörg Saßmannshausen <
[email protected]> wrote:
> Dear all,
>
> I am having a problem with a GAMESS output when I want to draw the
> HOMO/LUMO
> orbitals. I stumbled over it by chance when I was looking into the
> HOMO/LUMO
> of a large molecule and the problem can be repeated with a smaller molecule
> like water.
> I have attached the URL of the logfile from the GAMESS calculation
> <http://sassy-design.de/tmp/water-SP.log.gz> as well as the pictures
> of the HOMO, generated that way:
> frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5
> <http://sassy-design.de/tmp/homo.png>
> and mo 5, generated that way:
> frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5
> http://sassy-design.de/tmp/mo5.png
>
> As the list does not really like email attachments (for good reasons), in
> brief:
> MO5 should be the HOMO and when you draw it that way:
> frame 1.1; isosurface cutoff 0.05 mo 5 fill translucent 0.5
> you get the correct answer, i.e. that 'burger shaped' orbital with the two
> lobes being the bread and the molecule being the meat. :-)
> (see above link)
>
> However, using that command here:
> frame 1.1; isosurface cutoff 0.05 mo homo fill translucent 0.5
> i.e. calling the HOMO directly, gives a different and wrong picture. It
> looks
> more like higher, unoccupied orbital to me.
> (see above link)
>
> I am using jmol-12.0.49. I also tried the version Bob suggested in his
> email
> from the 22 Jun 2011 with the same results.
>
> Anybody got any ideas? That seems to be a bug to me, at least with the
> GAMESS
> output.
>
> All the best from a foggy London
>
> Jörg
>
> --
> *************************************************************
> Jörg Saßmannshausen
> University College London
> Department of Chemistry
> Gordon Street
> London
> WC1H 0AJ
>
> email: [email protected]
> web: http://sassy.formativ.net
>
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
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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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