Re: [phenixbb] elbow.builder

Problem solved: The OS X pre-compiled distribution comes with an executable gamess.Mar242007R1.x but the shell script seems to require gamess.00.x so in /usr/local/gamess I did this: sudo ln -s gamess.Mar242007R1.x gamess.00.x and benzene is as one would expect. BTW, when I run this under tcsh, I get a more informative error message -- it says it can't find gamess. Under zsh, it just says "Failed to read coordinates. Aborting optimisation." Anyway, it all works now. Thanks. Bill On Jun 3, 2007, at 3:08 PM, Peter Zwart wrote:

gamess is installed right?

P

2007/6/3, William Scott :

...

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:

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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?

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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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