I Stephen
I am confused, the problem is with Avogadro, or with the PyMOL's optimize
plugin <http://www.pymolwiki.org/index.php/Optimize>? I tried to replicate
the problem (with the plugin) and I get the correct answer (the chair
conformation)
Cheers,
Osvaldo
On Fri, Jul 10, 2015 at 11:04 AM, Stephen P. Molnar <s.mol...@sbcglobal.net>
wrote:
I have a bit of a strange problem. I have evaluated a number of Linux
> distributions in a VMware Player environment on my 64 bit laptop.
>
> I compile PyMol using the attached protocol.
>
> The OS is BioLinux v-8.0.5 with Avogadro Version 1.1.1
> Library Version 1.1.1
> Open Babel Version 2.3.2
> Qt Version 4.8.6
>
> The problem involves the Extensions/Optimize Geometry feature with
> cyclohexane as the test molecule. Cyclohexane as built is a planar
> molecule, but when I optimize the geometry it remains in a planar
> conformation. However in some of my test systems the geometry is returned
> as the chair isomer, which, of course, is correct!
>
> I will make the wild assumption (yes, I know how the word can be broken
> down) that there is a missing library. Which one might it be? Is any
> other information needed in order to address this rather nagging problem?
>
> Thanks in advance.
>
> --
> Stephen P. Molnar, Ph.D. Life is a fuzzy set
> www.FoundationForChemistry.com Stochastic and multivariate
> (614)312-7528 (c)
> Skype: smolnar1
>
>
>
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