AMBER Archive (2004)

Subject: Re: AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly?

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 07 2004 - 10:19:27 CDT

On Tue, Apr 06, 2004, Ilyas Yildirim wrote:
>
> I followed Joey Harriman's procedure, explained in
>
> http://amber.ch.ic.ac.uk/archive/200401/0155.html,
>
> to solve this problem. It looks like working ok. But I ended up with a
> lot of failure messages while running "make test.antechamber". Is this
> too normal? Some of the differences seem to be pretty big.

Without knowing more, it is hard to be sure. I have never had any luck
getting MOPAC 7 to work on my machines in a reliable fashion. You should
look carefully at the MOPAC output to make sure that the program has indeed
converged to a reasonable structure and wavefunction. There are sample
"mopac.out.save" files in the test directories that give "good" results.

>
> PS: It seems that the mopac.sh file needs to be changed a lot in order to
> modify antechamber to see MOPAC 7. I hope in AMBER 8, we wont have such a
> problem anymore.

Our best recommendations are the following:

For Amber 7: use the "minnesota" mopac, as suggested in the Users' Manual.
Then you don't have to edit the mopac.sh file, and you are more likely to
get useful results.

For Amber 8: mopac is no longer needed, as we provide our own semi-empirical
package (divcon).

...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu