[phenixbb] elbow.builder

Nigel W. Moriarty nwmoriarty at lbl.gov
Mon Jun 4 08:22:51 PDT 2007


Bill

Glad you could solve the problem of GAMESS.  I wasn't expecting too many 
people to use it so I'm glad you are making the effect.  GAMESS is a  
faster option (because many people have done a lot of work to make it 
so) and you can do higher level quantum calculations using

--basis 3-21G(d,p) --method mp2 (among others)

This can be extended so if you have problems or requests you should ask.

Regarding the documentation, we have a better script which missed the 
distribution and we'll work on the Mac problems also.

Nigel

William Scott wrote:
> 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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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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