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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 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/amberReceived on Tue Nov 01 2016 - 11:00:05 PDT