AMBER Archive (2008)

Subject: Re: AMBER: antechamber test failure

From: john smith (johnsmithgr8_at_gmail.com)
Date: Thu Oct 16 2008 - 00:53:50 CDT

Thanks for the reply,
Although the difference in the two values may be overlooked, there is one
more problem regarding the antechamber.
When I run the antechamber with protein, it give segmentation fault without
any information.
Antechamber is successful for small models with 3 amino residues but not for
the whole protein.
So what may be the reason for this?
-john

On 10/15/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:
>
> 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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