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