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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 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 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 Wed Sep 10 2014 - 17:00:03 PDT