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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Tue, Apr 5, 2022 at 1:23 AM Richard Kullmann <Richard.Kullmann.mpikg.mpg.de <mailto:Richard.Kullmann.mpikg.mpg.de>> wrote: Hello Ray, I had actually tried that as well, and got exactly the same error message...Considering that GB worked fine, I would also assume that the input prmtop and inpcrd files are fine. Is that correct? Best regards, Richard On 4/4/22 17:33, Ray Luo wrote: > Richard, > > How about you provide at least one option, such as "ipb=2," for the &pb > section, as in the &gb section of the input? > > Ray > -- > Ray Luo, Ph.D. > Professor of Structural Biology/Biochemistry/Biophysics, > Chemical and Materials Physics, Chemical and Biomolecular Engineering, > Biomedical Engineering, and Materials Science and Engineering > Department of Molecular Biology and Biochemistry > University of California, Irvine, CA 92697-3900 > > > On Mon, Apr 4, 2022 at 3:02 AM Richard Kullmann < > Richard.Kullmann.mpikg.mpg.de <mailto:Richard.Kullmann.mpikg.mpg.de>> wrote: > >> Hello, >> >> I am trying to run MMPBSA.py on my trajectories doing PB and GB >> calculations. Here is the input file I used for trying out the script: >> >> Input file for running PB and GB >> &general >> verbose=1, >> / >> &gb >> igb=2, >> / >> &pb >> / >> >> When calling it with a command of the form >> >> MMPBSA.py -O -i mmpbsa.in <http://mmpbsa.in> -cp com.top -rp rec.top -lp lig.top -y >> traj.crd , >> >> this is the final part of the output I get: >> >> Running calculations on normal system... >> >> Beginning GB calculations with >> /cluster/apps/amber20/gnu/amber20_src/bin/mmpbsa_py_energy >> calculating complex contribution... >> calculating receptor contribution... >> calculating ligand contribution... >> >> Beginning PB calculations with >> /cluster/apps/amber20/gnu/amber20_src/bin/mmpbsa_py_energy >> calculating complex contribution... >> File "/cluster/apps/amber20/gnu/amber20_src/bin/MMPBSA.py", line 100, >> in <module> >> app.run_mmpbsa() >> File >> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py", >> >> line 218, in run_mmpbsa >> self.calc_list.run(rank, self.stdout) >> File >> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", >> >> line 82, in run >> calc.run(rank, stdout=stdout, stderr=stderr) >> File >> "/cluster/apps/amber20/gnu/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", >> >> line 428, in run >> error_list = [s.strip() for s in out.split('\n') >> TypeError: a bytes-like object is required, not 'str' >> Exiting. All files have been retained. >> >> It seems that GB runs smoothly but PB doesn't. >> Do you have any idea what could be the issue here? >> Thank you very much in advance and best regards, >> >> Richard >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org <mailto:AMBER.ambermd.org> >> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber> >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org <mailto:AMBER.ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Apr 05 2022 - 09:00:17 PDT