[phenixbb] elbow.builder

William Scott wgscott at chemistry.ucsc.edu
Sun Jun 3 15:55:35 PDT 2007


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 <wgscott at chemistry.ucsc.edu>:
>> 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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>>



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