Re: [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files.

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 8 Sep 2014 15:22:12 -0700

Hi Jan-Philip,

Thanks a lot again for reporting! This is fixed in update.5. And the
master branch is finally corrected and this won't happen again. Let me
know if there is still problem after applying the updates.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Sep 8, 2014 at 6:57 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> Hello!
>
> There is this daunting problem in PBSA affecting me since three releases
> (AT12, 13, 14). Let's fix this, once and for all, please :).
>
> Short story, what needs to be done:
>
> 1) In AmberTools/src/pbsa/pb_force.F90, line 1438, change
>
>      call gen_dx_file(xm,ym,zm,h,gox,goy,goz,phi(1:xmymzm),&
>
> to
>
>      call gen_dx_file(xm,ym,zm,h,gox,goy,goz,frcfac*phi(1:xmymzm),&
>
> 2) Adjust test case AmberTools/test/pbsa_phiout.
>
>
> Long story:
>
> More than two years ago, I reported that electrostatic potential values
> are written to a DX file by PBSA in wrong units ("internal units"
> instead of kcal/(mol*e): http://archive.ambermd.org/201207/0466.html
>
> This was then fixed in AT12
> (http://ambermd.org/bugfixes/AmberTools/12.0/bugfix.17). The problem was
> re-introduced in AT13, and I reported again:
> http://archive.ambermd.org/201311/0380.html
>
> A fix for AT13 has unfortunately never been released (according to
> http://ambermd.org/bugfixesat.html).
>
> My hope now was on AT 14. A fix for AT14 is documented with "update.5:
> Fix a number of small bugs in PBSA" ... and "Potential printing was in
> the internal unit."
>
> Now that I compiled it and tried it out, I realized that PBSA is still
> behaving erroneously. The facts:
>
> - A test case was added, but someone did not properly check the numbers,
> and included a test case with the invalid values being the "golden
> standard".
> - The changelog of AT14 update.5 is out-of-sync with the actual code
> changes.
>
> How to verify that there is a problem:
>
> 1) Go to directory amber14/AmberTools/test/pbsa_phiout.
>
> 2) View file pbsa_phi.phi.save. The absolute value of most of the
> numbers is below 1. Particularly large absolute values are on the order
> of 10.
>
> 3) View pbsa_phi.dx.save. The absolute value of most of the numbers is
> on the order of 100. Particularly large absolute values are on the order
> of 1000.
>
> These are just two different file formats that should show the same
> numeric values. Actually, I have found this by investigating the system
> of which I know that electrostatic potential values of about 10
> kcal/(mol*e) are realistic, but the DX file just contains too large
> numbers. And indeed, the pb_force.F90 part of
> http://ambermd.org/bugfixes/AmberTools/12.0/bugfix.17 is just not
> applied in AT14. so it makes sense that we are back to old (erroneous)
> behavior.
>
>
> Hoping for a PBSA that is working out-of-the-box for my purposes.. :)
>
> Cheers!
>
> Jan-Philip
>
>
>
>
>
>
>
>
>
>
>
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Received on Mon Sep 08 2014 - 15:30:02 PDT