Re: [AMBER-Developers] sander.APBS broken

From: Mark Williamson <>
Date: Tue, 23 Mar 2010 14:27:42 -0700

Jason Swails wrote:
> On Sun, Mar 21, 2010 at 7:33 PM, Jason Swails <> wrote:
>> Hello,
>> As a follow-up, I'm assuming all that was changed was ener%vdw to
>> pot%vdw, which is one of the changes that I tested out. EPB and ELE
>> are getting exchanged, which I'm trying to hunt down in
>> printe.f/force.f. This results in what appears to be a simple
>> *switch* of ELE and EPB values for the Na+, Cl-, etc. ion test cases
>> for iapbs_radi tests. (Moreover, a non-zero ELE value for a single
>> particle, even if charged, makes no sense, so this must be backwards).
>> However, when actual amino acids are calculated, the EPB from the
>> save files matches exactly the EEL being printed out, but EPB from the
>> save files does NOT match EEL being printed out -- this value is
> The last statement is backwards (EEL from save does NOT match EPB
> printed out. I just said p and not p and exploded in a mist of
> logical impossibility).
>> getting lost somewhere. This causes deviations in the total energy
>> equal to the amount by which EEL and EPB are off from one another.
>> I've attached my relative TEST_FAILURES.diff file.
>> Thanks!
>> Jason

I finally managed to get APBS and the iAPSB interface working, hence I
was able to test my speculative fixes locally. So, all fixed, tested and
checked in. Robert Konecny also informs me that he has had joy with my
patch as well. Let me know if there are any more issues.


Mark Williamson, Post Doc
Walker Molecular Dynamics Group
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email:  mjw at
Office: 858-246-0827
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Received on Tue Mar 23 2010 - 14:30:03 PDT
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