Re: [phenixbb] elbow.builder

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 :

...

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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-- 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 : [email protected] Web : CCI.LBL.gov