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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 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/amberReceived on Tue Nov 01 2016 - 09:30:02 PDT