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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 Sat, Mar 12, 2016 at 11:07 AM, Arati Paudyal <apsilwal123.gmail.com> wrote: > Dear all, > > When I run MMGB/PBSA wiht the following input, I got the following error > message at some point. But when I change the interval to 4 or 5 the > calculation runs fine with out any problem. I got same error message if I > go to 2. ( I have not done 1). The error says there is problem in topology > file but it is little bit weird that the same topology file is good for the > other cases but not when you change the interval. I would really appreciate > if you could give your opinion on whats going on here. > > &general > startframe=500, endframe=3500, interval=3, > verbose=2, keep_files=2, strip_mask=':WAT,CL', > / > &gb > igb=8, saltcon=0.150, > / > &pb > inp=1, radiopt=0, istrng=0.15, fillratio=4.0 > / > > Error message: > > Loading and checking parameter files for compatibility... > mmpbsa_py_energy found! Using > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy > cpptraj found! Using > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/cpptraj > Preparing trajectories for simulation... > 834 frames were processed by cpptraj for use in calculation. > > Running calculations on normal system... > > Beginning GB calculations with > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy > calculating complex contribution... > calculating receptor contribution... > calculating ligand contribution... > > Beginning PB calculations with > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy > calculating complex contribution... > 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/software/Amber/14Tools15--Intel-13.0.1.117/bin/MMPBSA.py", > line 104, in <module> > app.run_mmpbsa() > File > "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/main.py", > line 218, in run_mmpbsa > self.calc_list.run(rank, self.stdout) > File > "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", > line 82, in run > calc.run(rank, stdout=stdout, stderr=stderr) > File > "/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", > line 431, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: > /opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/mmpbsa_py_energy failed > with B.prmtop! > _______________________________________________ > 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 Mar 12 2016 - 20:30:03 PST