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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, Nov 1, 2016 at 12:14 PM, Marek Maly <marek.maly.ujep.cz> wrote: > Hi Ray, > > sorry but keyword "epsout" is not listed as the valid > one for "&pb namelist variables" in MMPBSApy/Amber16 manual. > > The only one listed relevant keyword is here "exdi" but anyway > I tried PB calculation with both A) "exdi=1" and B)"epsout=1" with > "use_sander=1". > > In case of A) mmpbsa.out stays empty in case of B) the same problem as > in case of using default "mmpbsa_py_energy". > > With using sander_apbs it works as I already wrote. > > Entropy calc. ends with errors because of the minimization function as you > can > see by yourself when testing my prmtop/mdcrd files. > > Best wishes, > > Marek > > > > > > > > > > > > Dne Tue, 01 Nov 2016 18:49:36 +0100 Ray Luo <rluo.uci.edu> napsal/-a: > >> Marek, >> >> I can set epsout=1 for pbsa, so I think the option of use_sander >> should work. The default setup uses nab, which is quite limited and is >> hard to trace what went wrong because there is no output recorded. >> >> Ray >> -- >> Ray Luo, Ph.D. >> Professor >> Biochemistry, Molecular Biophysics, Chemical Physics, >> Chemical and Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> >> >> On Tue, Nov 1, 2016 at 10:36 AM, Marek Maly <marek.maly.ujep.cz> wrote: >>> Thank you Ray, >>> >>> According to Amber16 manual "exdi" is listed only as a >>> MMPBSApy parameter in "&pb namelist variables" >>> not in "&gb namelist variables". >>> >>> So that is the reason why I did not use this parameter >>> in my gb calculation. Anyway pb calculation should work for >>> any value of external el. permitivity const. I guess. >>> >>> Yes for this moment I need just vacuum energy terms so >>> I am OK with gb one because those should be the same >>> for gb and pb but later I will need also calculate >>> energies of systems containing "Dodecyltrimethylammonium bromide" >>> in water. >>> >>> With serial version of MMPBSA (MMPBSA.py) there are identical problems >>> as with the parallel one. >>> >>> I now installed apbs support to have possibility to use sander_apbs >>> with MMPBSA.py environment and it works ! >>> >>> But of course would be a good idea to solve this problem also in >>> default Amber PB solver. >>> >>> Moreover there is that problem also for entropy calculation where >>> in the first place should be corrected xmin() procedure. >>> >>> I will send you relevant prmtops/mdcrd files off-line so you can >>> reproduce reported errors and eventually fix it. >>> >>> Best wishes, >>> >>> Marek >>> >>> >>> >>> >>> >>> Dne Tue, 01 Nov 2016 17:14:50 +0100 Ray Luo <rluo.uci.edu> napsal/-a: >>> >>>> Marek, >>>> >>>> I see that you are setting exdi = 1 in PB, but not in GB. Is there any >>>> reason doing so? Do you want to do a vacuum run with PB? What about >>>> the non-MPI run? >>>> >>>> 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 Tue, Nov 1, 2016 at 8:54 AM, Marek Maly <marek.maly.ujep.cz> wrote: >>>>> Hi All, >>>>> >>>>> After recent upgrade to Amber 16 I wanted to calculate very simply >>>>> thing. >>>>> Binding energy between Br anion and Dodecyltrimethylammonium in >>>>> Dodecyltrimethylammonium bromide molecular complex >>>>> ( see >>>>> http://www.sigmaaldrich.com/catalog/product/sigma/d5047?lang=en®ion=CZ >>>>> ). >>>>> I used MMPBSA.py.MPI for this calculation (6 threads). >>>>> >>>>> >>>>> I tried #1 GB calculation #2 PB calculation and #3 TdS calucaltion >>>>> (entropic contribution). >>>>> >>>>> Interestingly I succeeded just in case of GB calculation the rest was >>>>> finished >>>>> with errors. >>>>> >>>>> I am naturally asking why ? and what to try to do to eliminate those >>>>> errors. >>>>> Please see input/output files below and thank you in advance for your >>>>> suggestions. >>>>> >>>>> >>>>> In case of PB calculation I have obtained errors which were printed >>>>> directly to the screen >>>>> >>>>> ---------------------------------------- >>>>> /opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631: >>>>> UserWarning: Solvated topology 0 has IFBOX == 0 >>>>> warn('Solvated topology %s has IFBOX == 0' % ifbox) >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> Warning: inp=1 was old default >>>>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.0050 >>>>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to >>>>> inp=1 default value: 0.000 >>>>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 >>>>> default >>>>> value: 1.400 >>>>> File "/opt/amber16/bin/MMPBSA.py.MPI", line 100, in <module> >>>>> app.run_mmpbsa() >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", >>>>> line 218, in run_mmpbsa >>>>> self.calc_list.run(rank, self.stdout) >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", >>>>> line 82, in run >>>>> calc.run(rank, stdout=stdout, stderr=stderr) >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", >>>>> line 431, in run >>>>> self.prmtop) + '\n\t'.join(error_list) + '\n') >>>>> CalcError: /opt/amber16/bin/mmpbsa_py_energy failed with prmtop >>>>> ../../prmtop/COM.prmtop! >>>>> >>>>> ---------------------------------------- >>>>> >>>>> I would like just to notice that All 3 calculations are using >>>>> identical >>>>> set of promtop files >>>>> (COM.prmtop, LIG.prmtop, REC.prmtop) which are in one central folder. >>>>> >>>>> >>>>> In case of TdS calculation I have obtained errors which were printed >>>>> directly to the screen >>>>> >>>>> ---------------------------------------------- >>>>> ERROR in xmin(): Too few atoms. >>>>> >>>>> ERROR in xmin(): Too few atoms. >>>>> >>>>> ERROR in xmin(): Too few atoms. >>>>> >>>>> ERROR in xmin(): Too few atoms. >>>>> >>>>> ERROR in xmin(): Too few atoms. >>>>> >>>>> ERROR in xmin(): Too few atoms. >>>>> File "/opt/amber16/bin/MMPBSA.py.MPI", line 108, in <module> >>>>> app.parse_output_files() >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", >>>>> line 942, in parse_output_files >>>>> self.INPUT['verbose'], self.using_chamber) >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", >>>>> line 999, in __init__ >>>>> self.delta2() >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", >>>>> line 1232, in delta2 >>>>> self.lig.data[key].avg(), >>>>> File >>>>> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", >>>>> line 187, in avg >>>>> return (sum(self) / len(self)) >>>>> ZeroDivisionError: integer division or modulo by zero >>>>> Error occured on rank 0. >>>>> Exiting. All files have been retained. >>>>> >>>>> ---------------------------------------------- >>>>> >>>>> This suggests that routine xmin() has problem with 1-atom residues >>>>> (here >>>>> Ligand Br-). >>>>> There is clearly missing this trivial branch which simply in such >>>>> cases >>>>> does not apply any >>>>> minimization (because there is nothing to minimize at all in such >>>>> case) >>>>> and just return the input "configuration". >>>>> >>>>> >>>>> I would like just to notice that the similar problems I had when I >>>>> wanted >>>>> to >>>>> calculate binding energy between complete "Dodecyltrimethylammonium >>>>> bromide" >>>>> complex and another molecule. The following rows indicates that if >>>>> part >>>>> of analysed system is/are ion/ions i.e. 1-atom residuum, there might >>>>> be >>>>> problems (PB, TdS calc.) also because some procedures simply do not >>>>> count >>>>> with such cases. >>>>> >>>>> >>>>> Thank you in advance ! >>>>> >>>>> Best wishes, >>>>> >>>>> Marek >>>>> >>>>> INPUT/OUTPUT files >>>>> >>>>> #1 - GB >>>>> >>>>> INPUT (mmpbsa.in) >>>>> ----------------------------------------- >>>>> MMPBSA.py input file for running GB >>>>> &general >>>>> interval=10,startframe=1 >>>>> keep_files=1, debug_printlevel=2 >>>>> / >>>>> &gb >>>>> igb=1, saltcon=0.0 >>>>> / >>>>> >>>>> -------------------------------------------- >>>>> >>>>> OUTPUT (mmpbsa.out) >>>>> ------------------------------------------- >>>>> Loading and checking parameter files for compatibility... >>>>> mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy >>>>> cpptraj found! Using /opt/amber16/bin/cpptraj >>>>> Preparing trajectories for simulation... >>>>> 100 frames were processed by cpptraj for use in calculation. >>>>> >>>>> Running calculations on normal system... >>>>> >>>>> Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy >>>>> calculating complex contribution... >>>>> calculating receptor contribution... >>>>> calculating ligand contribution... >>>>> >>>>> Timing: >>>>> Total setup time: 0.016 sec. >>>>> Creating trajectories with cpptraj: 0.048 sec. >>>>> Total calculation time: 0.066 sec. >>>>> >>>>> Total GB calculation time: 0.061 sec. >>>>> >>>>> Statistics calculation & output writing: 0.005 sec. >>>>> Total time taken: 0.146 sec. >>>>> >>>>> >>>>> MMPBSA.py Finished! Thank you for using. Please cite us if you publish >>>>> this work with this paper: >>>>> Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. >>>>> Gohlke, >>>>> H. and Roitberg, A. E. >>>>> J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321 >>>>> >>>>> >>>>> ------------------------------------------- >>>>> >>>>> >>>>> #2 - PB >>>>> >>>>> INPUT (mmpbsa.in) >>>>> ----------------------------------------- >>>>> MMPBSA input file for running PB >>>>> &general >>>>> interval=10,startframe=1 >>>>> keep_files=1, debug_printlevel=2 >>>>> / >>>>> &pb >>>>> istrng=0.0, inp=1, >>>>> radiopt=0, exdi=1, >>>>> / >>>>> #&decomp >>>>> #cavity_surften=0.00542 >>>>> >>>>> >>>>> #idecomp=2, dec_verbose=0 >>>>> #/ >>>>> -------------------------------------------- >>>>> >>>>> OUTPUT (mmpbsa.out) >>>>> ------------------------------------------- >>>>> Loading and checking parameter files for compatibility... >>>>> mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy >>>>> cpptraj found! Using /opt/amber16/bin/cpptraj >>>>> Preparing trajectories for simulation... >>>>> 100 frames were processed by cpptraj for use in calculation. >>>>> >>>>> Running calculations on normal system... >>>>> >>>>> Beginning PB calculations with /opt/amber16/bin/mmpbsa_py_energy >>>>> calculating complex contribution... >>>>> >>>>> =================================================================================== >>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >>>>> = PID 16649 RUNNING AT dyn-138-272.ujep.cz >>>>> = EXIT CODE: 1 >>>>> = CLEANING UP REMAINING PROCESSES >>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >>>>> =================================================================================== >>>>> >>>>> ------------------------------------------- >>>>> >>>>> #3 - TdS >>>>> >>>>> INPUT (mmpbsa.in) >>>>> ----------------------------------------- >>>>> MMPBSA input file for running per-residue decomp >>>>> &general >>>>> startframe=1 >>>>> keep_files=1, debug_printlevel=2, >>>>> / >>>>> &nmode >>>>> nmode_igb=0, nmode_istrng=0.0, nminterval=167, >>>>> maxcyc=10000, drms=0.1, >>>>> / >>>>> -------------------------------------------- >>>>> >>>>> OUTPUT (mmpbsa.out) >>>>> ------------------------------------------- >>>>> Loading and checking parameter files for compatibility... >>>>> cpptraj found! Using /opt/amber16/bin/cpptraj >>>>> mmpbsa_py_nabnmode found! Using /opt/amber16/bin/mmpbsa_py_nabnmode >>>>> Preparing trajectories for simulation... >>>>> 1000 frames were processed by cpptraj for use in calculation. >>>>> 6 frames were processed by cpptraj for nmode calculations. >>>>> >>>>> Running calculations on normal system... >>>>> >>>>> Beginning nmode calculations with /opt/amber16/bin/mmpbsa_py_nabnmode >>>>> calculating complex contribution... >>>>> calculating receptor contribution... >>>>> calculating ligand contribution... >>>>> >>>>> =================================================================================== >>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >>>>> = PID 16821 RUNNING AT dyn-138-272.ujep.cz >>>>> = EXIT CODE: 1 >>>>> = CLEANING UP REMAINING PROCESSES >>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >>>>> =================================================================================== >>>>> >>>>> ------------------------------------------- >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery: >>>>> http://www.opera.com/mail/ >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> -- >>> Tato zpráva byla vytvořena převratným poštovním klientem Opery: >>> http://www.opera.com/mail/ >>> >>> _______________________________________________ >>> 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 > > > -- > Tato zpráva byla vytvořena převratným poštovním klientem Opery: > http://www.opera.com/mail/ > > _______________________________________________ > 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 Nov 01 2016 - 14:00:02 PDT