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: Wed, 10 Sep 2014 16:53:11 -0700

Hi Jan-Philip,

It turns out that the specific file and test cases were committed to
the master branch but were not included in the patch. My student is
generating a new patch to put these updates into amber14.

Thanks again for pointing this out!

Ray
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Sep 9, 2014 at 12:28 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Really, I'll take a look of update.5 and the output files again …
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Tue, Sep 9, 2014 at 3:28 AM, Jan-Philip Gehrcke
> <jgehrcke.googlemail.com> wrote:
>> Hey Ray,
>>
>> Thanks for the quick response! I do not understand how you have released
>> or will release that update. As described, AT14 update.5 missed to fix
>> named issue. Are you saying that you want to release an update for
>> update.5? The version of
>> http://ambermd.org/bugfixes/AmberTools/14.0/update.5 that I retrieve
>> right now does not address the problem.
>>
>> Cheers!
>>
>> On 09/09/2014 12:22 AM, Ray Luo, Ph.D. wrote:
>>> 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 Wed Sep 10 2014 - 17:00:03 PDT
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