AMBER Archive (2008)

Subject: Re: AMBER: antechamber test failure

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Oct 15 2008 - 08:16:06 CDT

On Tue, Oct 14, 2008, john smith wrote:
>
> I am currently using Amber on my Intel Pentium IV with 1GB RAM with RedHat
> Linux EL4.
> I have compiled AmberaTools with gcc, and Amber serial version with intel
> fortran compiler (ifort).
> However, when i run the AmberTools test, i get many Possible FAILURE's for
> antechamber.
> The entries in TEST_FAILURES.diff are
>
> possible FAILURE: check ash.mol2.dif
>
> /opt/amber10/test/antechamber/ash
>
> 8c8
>
> < 2 CH3 2.0000 2.0900 0. c3 1 ACE -0.172000
>
> > 2 CH3 2.0000 2.0900 0. c3 1 ACE -0.172600
>

...etc

These all look like very small changes in charges (less than 0.01 electron),
which are expected differences between compilers.

The am1-bcc scheme first minimizes the geometry, then computes charges.
Slight differences in when the minimization terminates can lead to slight
differences in the final charges.

...dac

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