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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Sat, May 24, 2014 at 10:37 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote: > Hello, > > looking at the update list on http://ambermd.org/bugfixesat.html I don't > think this patch has ever been released for AT 13. Is that true? Is the > behavior fixed in AT 14? > > > Cheers, > > Jan-Philip > > On 03.12.2013 21:21, wmsmith.uci.edu wrote: >> The patch you mentioned was constructed, but its changes were not yet >> pushed to the branch as we are awaiting approval. I can easily amend the >> patch so that pb_read will no longer force radiopt = 2 when phiout=1 and >> will instead display a warning if it is set to some other value. >> Be aware that if you use radiopt other than 2, it will be up to you to >> find and use the appropriate atomic radii in your visualization software >> since the molecular surface will no longer correspond to the one defined >> by the radii in your topology file... If you use the levelset description >> (current default I believe), you can always print out the level set as a >> dx file. If not, you will have to construct the surface yourself. >> -Wes >>> Jan-Philip, >>> >>> Wes has submitted the patch. I think it's pending approval … >>> >>> Also as for radiopt upon the printout of phi map, we can certainly do it >>> as >>> you suggested … The original argument for hardwiring the radii for >>> visualization is this. It is not straightforward to set radii in VMD/PyMol >>> and the phi map is supposed to use values on the outside of the molecular >>> surface, i.e. solvated phi values since the purpose is to get some >>> intuition on the effect of a molecular probe approaching the surface from >>> the outside. Thus we want the best possible match between the radii used >>> in >>> the visualization software and PBSA. Furthermore. PBSA reduces the radii >>> by >>> 0.1 A to make sure the projected phi values on the molecular surfaces are >>> solvated values. >>> >>> However, this is not necessary when the newer DX volumetric data output >>> from Amber is used for surface rendering. The plan is that we'll still set >>> radiopt == 2 as the default condition and remind users to reset radii in >>> the visualization software to those used by Amber if radiopt != 2. >>> >>> Ray >>> >>> -- >>> Ray Luo, Ph.D. >>> Professor, >>> Biochemistry, Molecular Biophysics, and >>> Biomedical Engineering >>> University of California, Irvine, CA 92697-3900 >>> >>> >>> On Tue, Dec 3, 2013 at 4:54 AM, Jan-Philip Gehrcke >>> <jgehrcke.googlemail.com>wrote: >>> >>>> Hello Wes and Ray, >>>> >>>> thanks for your immediate feedback. I have seen that you have a patch >>>> since last week -- any news about when this will be made public? >>>> >>>> Also, I would like to discuss again the fact that radiopt is internally >>>> overridden to 2 when phiout == 1. In understand that there were some >>>> arguments for taking this decision. However, in my opinion, the current >>>> behavior must be changed for two reasons: >>>> >>>> - the current behavior contradicts documentation. The docs say that via >>>> radiopt = 1 PBSA uses the radii from the prmtop file. When no error >>>> appears as of a missing atom type, the user has no chance to realize >>>> that PBSA magically decided to use its hard-coded radii rather than the >>>> ones from the prmtop. >>>> >>>> - one could fix the docs or the code -- I vote for code. There should be >>>> a way to make PBSA take radii from the prmtop file *without being forced >>>> to manually change code*. And I don't see why this statement should be >>>> invalid depending on an output format. >>>> >>>> >>>> Thanks a lot for looking into this, >>>> >>>> Jan-Philip >>>> >>>> >>>> On 11/26/2013 07:49 PM, Ray Luo, Ph.D. wrote: >>>>> Jan-Philip, >>>>> >>>>> Okay, it turns out someone overwrote that change in the AmberTools13 >>>>> release. Wes will need to issue a patch to put it back. >>>>> >>>>> Thanks a lot for reporting! >>>>> >>>>> Ray >>>>> >>>>> -- >>>>> Ray Luo, Ph.D. >>>>> Professor, >>>>> Biochemistry, Molecular Biophysics, and >>>>> Biomedical Engineering >>>>> University of California, Irvine, CA 92697-3900 >>>>> >>>>> >>>>> On Mon, Nov 25, 2013 at 10:52 AM, Jan-Philip Gehrcke < >>>>> jgehrcke.googlemail.com> wrote: >>>>> >>>>>> On 11/25/2013 07:13 PM, Ray Luo, Ph.D. wrote: >>>>>>> Jan-Philip, >>>>>>> >>>>>>> Indeed, when you ask for potential printout, pbsa would set radii as >>>> used >>>>>>> in VMD for consistency. That's why it overwrites your option in the >>>> input >>>>>>> file. If you insist in using radiopt=0, you can certainly comment >>>> the >>>>>> line >>>>>>> "radiopt=2" output and do it again. >>>>>>> >>>>>>> Ray >>>>>> >>>>>> Hey Ray, >>>>>> >>>>>> thanks for the confirmation. Two things left to be discussed: >>>>>> >>>>>> 1) I outcommented radiopt=2. In another attempt I left it as is and >>>>>> simply added the missing atom types to phi_aaradii(). In both cases, >>>>>> pbsa runs without error and produces the same result. So far so good. >>>>>> However, I end up with electrostatic potential values that seem to be >>>>>> too large by about two orders of magnitude. >>>>>> >>>>>> I have used pbsa earlier (1-2 years ago, from AmberTools12), with >>>>>> basically the same input (radiopt=0 is the only difference here) >>>> where I >>>>>> got values between 1 and 10 kcal/mol for most of the space regions >>>> near >>>>>> the protein surface. Now, I get something between 500 and 2000 >>>> (whatever >>>>>> units). So, the units seem to have changed. >>>>>> >>>>>> Back in 2012, we also had an issue with the estatic potential units >>>> in >>>>>> the DX output file: http://archive.ambermd.org/201207/0466.html. At >>>>>> these times, Wes took care of this and released a bug fix making sure >>>>>> that the unit would be kcal/(mol*e). Did this accidentally change >>>> again? >>>>>> >>>>>> I have further proof that something changed. Found the >>>>>> AmberTools12-based pbsa binary that I used earlier. I used both, the >>>> old >>>>>> binaries and the new binaries with *the same input*. The first few >>>>>> values of the DX file corresponding to the old binary: >>>>>> >>>>>> 1.3067049144E+00 1.3232708113E+00 1.3399177244E+00 >>>>>> 1.3566168815E+00 1.3733524282E+00 1.3900526596E+00 >>>>>> >>>>>> Using the new AmberTools13-based pbsa binary: >>>>>> >>>>>> 5.4732938513E+02 5.5427901231E+02 5.6121241210E+02 >>>>>> 5.6816177213E+02 5.7512228560E+02 5.8210218482E+02 >>>>>> >>>>>> The factor is about 418. >>>>>> >>>>>> >>>>>> 2) I would suggest to change the current code behavior, because >>>>>> otherwise what happens is entirely intransparent to the user (we >>>> define >>>>>> radiopt=0 and magically get something undocumented). Would it be >>>>>> possible to use pymol/vmd-radii only in case radiopt was not >>>> explicitly >>>>>> defined in the input file (as kind of fallback)? Then, one should >>>> also >>>>>> add a corresponding warning/information to the output file, that >>>> these >>>>>> radii will now be applied. A missing-radius-error right after such an >>>>>> info line would make sense. >>>>>> >>>>>> >>>>>> Thanks for your support, >>>>>> >>>>>> Jan-Philip >>>>>> >>>>>> >>>>>>> >>>>>>> -- >>>>>>> Ray Luo, Ph.D. >>>>>>> Professor, >>>>>>> Biochemistry, Molecular Biophysics, and >>>>>>> Biomedical Engineering >>>>>>> University of California, Irvine, CA 92697-3900 >>>>>>> >>>>>>> >>>>>>> On Mon, Nov 25, 2013 at 10:04 AM, Jan-Philip Gehrcke < >>>>>>> jgehrcke.googlemail.com> wrote: >>>>>>> >>>>>>>> On 11/25/2013 06:38 PM, Jan-Philip Gehrcke wrote: >>>>>>>> >>>>>>>>> I used 'set default pbradii bondi' in leap when creating that >>>> topology >>>>>>>>> file. I am using AmberTools 13 with the latest patches for pbsa. >>>> The >>>>>>>>> whole pbsa input file is this: >>>>>>>>> >>>>>>>>> &cntrl >>>>>>>>> inp=0, >>>>>>>>> / >>>>>>>>> &pb >>>>>>>>> npbopt=0, >>>>>>>>> radiopt=0, >>>>>>>>> npbverb=0, >>>>>>>>> space=1, >>>>>>>>> fillratio=1.0, >>>>>>>>> sasopt=2, >>>>>>>>> phiout=1, >>>>>>>>> phiform=2, >>>>>>>>> npbverb=1, >>>>>>>>> / >>>>>>>>> >>>>>>>>> So, what is the issue here? Why is the given radius not used? >>>>>>>>> >>>>>>>> >>>>>>>> In pb_read.F90 there is this code: >>>>>>>> >>>>>>>> ! set phimap output options when requested >>>>>>>> >>>>>>>> if ( phiout == 1 ) then >>>>>>>> outphi = .true. >>>>>>>> radiopt = 2 >>>>>>>> donpsa = .false. >>>>>>>> npopt = 0 >>>>>>>> end if >>>>>>>> >>>>>>>> >>>>>>>> Since I am using phiout=1, radiopt becomes set to the >>>> (undocumented) >>>>>>>> value 2, which in turn makes pb_init() end up in this section: >>>>>>>> >>>>>>>> else if ( radiopt == 2 ) then >>>>>>>> call phi_aaradi( natom, isymbl, radi ) >>>>>>>> >>>>>>>> So, if this quick analysis is right, the question would be why we >>>> set >>>>>>>> radiopt = 2 when phiout == 1. >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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/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/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 Sat May 24 2014 - 12:00:02 PDT