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-- 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Sep 09 2014 - 12:30:03 PDT