[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
>
>
>
>



More information about the phenixbb mailing list