Re: [AMBER] Ambertools14 sander_pbsa_decres test failure

From: Ray Luo, Ph.D. <>
Date: Fri, 19 Sep 2014 10:27:39 -0700


Turns out it has been fixed in the master branch. Will ask Wes to
generate a patch for amber14 as well.

All the best,
Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Sep 3, 2014 at 6:12 PM, David A Case <> wrote:
> On Wed, Sep 03, 2014, Shan-ho Tsai wrote:
>> I have just installed the serial version of Amber14
>> (with updates 1 to 5 installed) and AmberTools14 (with
>> updates 1 to 11 installed) using the gnu 4.7.1 compilers
>> on our Linux cluster (64-bit RHEL5). All Amber14 tests
>> passed, but the sander_pbsa_decres test in the AmberTools
>> test suite failed (all other AmberTools tests passed).
>> The differences from the output file provided are very
>> large (see below).
> Thanks for the report.  We are aware of this, and the bug is entered into
> bugzilla (bug #282).  It's been a busy time, and no one has yet been able to
> track it down.  If you plan to look a decomposition of PB energies, you should
> take care.
> ....dac
> [General caveat about such energy decompositions: (1) they are approxiate
> and somewhat arbitrary; (2) if you decompose numbers enough different ways,
> you increase your chances of being fooled by finding some combination of terms
> that appears to explain some trend.]
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Received on Fri Sep 19 2014 - 10:30:02 PDT
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