Re: [AMBER] comparison failures in the Amber11 and AT15 test

From: Jason Swails <>
Date: Fri, 11 Nov 2011 22:22:41 -0500

If you ran the script, it printed this at the bottom:

NOTE: Because PBSA has changed since Amber 11 was released, some
tests are known to fail and others are known to quit in error. These
can be safely ignored.

Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc
   Run.argasp.min Run.dadt.min Run.dgdc.min
   Run.lysasp.min Run.polyALA.min Run.polyAT.min
   Run.argasp.min Run.dadt.min Run.dgdc.min
   Run.lysasp.min Run.polyALA.min Run.polyAT.min
   Run.argasp.min Run.dadt.min Run.dgdc.min
   Run.lysasp.min Run.polyALA.min Run.polyAT.min

Tests that produce possible FAILUREs:
   cd sander_pbsa_ipb2 && ./Run.110D.min
   cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here)
   cd sander_pbsa_tsr && ./Run.tsrb.min
   cd sander_pbsa_decres && ./Run.pbsa_decres tests 02, 03, and 05

Also note that you'll have much better luck getting support for problems
with MM/PBSA analyses if you use the Python version of the script
(, which is part of AmberTools 1.5).


On Fri, Nov 11, 2011 at 6:20 PM, bin wang <> wrote:

> Dear Amber users,
> I have a question regarding the test of Amber11 and AT15.
> After installation of AT15 and Amber11, I run make test and get the .diff
> files in folder $AMBERHOME/AmberTools/test/logs/test_at_serial and
> $AMBERHOME/test/logs/test_amber_serial. The results showed some comparison
> failures. Especially, there are some possible failures in
> test/sander_pbsa_radi, test/sander_pbsa_tsr, test/sander_pbsa_decres,
> test/sander_pbsa_decpw, and src/mm_pbsa/Examples. But I need to use pbsa
> to calculate binding energy. I am wondering if these failures are
> significant problems? Can I still use mm_pbsa or I have to fix it?
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Nov 11 2011 - 19:30:05 PST
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