[phenixbb] elbow.builder
William Scott
wgscott at chemistry.ucsc.edu
Sun Jun 3 14:44:04 PDT 2007
actually, "small distortions" was too optimistic:
http://chemistry.ucsc.edu/~wgscott/temp/benzene.png
On Jun 3, 2007, at 2:33 PM, William Scott wrote:
> Hi folks:
>
> I've been playing around a bit with elbow.builder, and found the
> following:
>
> --------------
>
>
> elbow.builder --opt --smiles c1ccccc1
>
> gives me a nice, flat, hexagonal benzene
>
> elbow.builder --gamess --smiles c1ccccc1
>
> gives me a benzene that is slightly bent out of plane and has other
> small distortions with respect to 6-fold symmetry.
>
> Is this a problem with elbow, a problem with gamess, or a Jahn-
> Teller effect?
>
>
> ------------
>
>
>
> Also, I noticed elbow.doc requires a mozilla or netscape
> executable. Since both of these are obsolete, maybe a firefox
> executable should be an option? On OS X, "open" should open a URL
> in the user's favorite browser, but it doesn't seem to work right
> with Safari (which stupidly opens a Finder window of the directory
> containing the html file). My workaround was to make a shell
> script called "mozilla" that invokes Camino:
>
> #!/bin/zsh -f
> /usr/bin/open -a Camino "$@"
>
> HTH someone.
>
> ------------------
>
>
> Bill
>
>
>
>
> William G. Scott
>
> contact info: http://chemistry.ucsc.edu/~wgscott
>
>
>
>
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