AMBER Archive (2003)

Subject: RE: AMBER: antechamber test failure

From: Meg McCarrick (mmccarrick_at_celgene.com)
Date: Tue Nov 18 2003 - 11:06:12 CST

Dave,

Thanks for your reply, but I resolved the problem late yesterday. My
version of MOPAC seems to require a space before the first two input lines,
so I changed the text in antechamber.c to " AM1 MMOK... from the original
"AM1 MMOK... and did the same with the second line. You may want to modify
the distributed code if this syntax will work for all MOPAC versions. The
test jobs are working fine now.

Regards, Meg

-----Original Message-----
From: David A. Case [mailto:case_at_scripps.edu]
Sent: Monday, November 17, 2003 7:04 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: antechamber test failure

On Mon, Nov 17, 2003, Meg McCarrick wrote:

> I edited mopac.sh in the src/antechamber directory and the exe directory
to
> point toward my Mopac distribution. When I run the test job in the
> test/antechamber/ directory, all of the tests fail. The test jobs in the
> Mopac distribution directory all succeed. I am using Mopac509mn. Do you
> know what could be causing this problem?
>

What is the nature of the "failure"? Is it just slight differences in the
charges (which, unfortunately, is to be expected, since mopac does not give
consistent results on various computer platforms)? Or is it something more
serious, such as assignment of different atom types, and so on?

We would need to get more details, such as the *.dif files, to be of much
help here.

..regards...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
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