AMBER Archive (2004)

Subject: Re: AMBER: installation test question (antechamber, ash)

From: David A. Case (
Date: Mon Jan 26 2004 - 14:24:26 CST

On Mon, Jan 26, 2004, Charles F. Fisher wrote:

> I am installing AMBER on an HP ia64 system. I also installed the MOPAC
> version from When doing the antechamber
> tests, several diffs show relatively large differences ( e.g.
> 6.04980360E+00 vs. 6.10447050E+00 in the prmtop files). I am including the
> problematic diff files from the ash test in this email. Are these tests
> within acceptable limits, or does this indicate a problem?

Charges in the prmtop file are in internal units, which are 18.2 times greater
than charges in atomic units. Hence, the diff above (6.05 vs. 6.10)
corresponds to a change of .05/18.2 = 0.003 charge units. This is not an
unexpected difference.

The problem arises from the fact that the bcc charge model does a geometry
optimization before calculating charges, and (with the convergence criteria
we use) the optimization halts at slightly different points on different
machines. We are exploring using tighter convergence criteria for the next
release, but even that is not entirely simple.

A small difference in charge model is physically not important, but it is
a pain if one is trying to root out problems with the code. My best guess
is that you are not seeing any real problems here.

..good luck...dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to