[phenixbb] elbow.builder

[William Scott]

Nigel W. Moriarty wrote:
> 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.

With examples like these, how could anyone resist?

zsh-% elbow.get_smiles
_______________________________________________________________________________
 [ADM] adamantane          [CHX] cyclohexane         [MOI] morphine
 [ATP] atp                 [CIA] cialis              [NCT] nicotine
 [BCR] beta_carotene       [COC] cocaine             [PN1] ampicillin
 [BNZ] benzene             [EHN] ethane              [VIT] vitamin_e
 [CFF] caffeine            [FRU] fructose
_______________________________________________________________________________


You may have just enabled computational quantum chemistry for the masses...

> 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
>
>