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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 1:29 PM, Ray Luo <rluo.uci.edu> wrote: > Okay, I'm looking at your data file to reproduce the problem ... > > 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 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 - 15:00:02 PDT