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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 Wed, Apr 6, 2022 at 2:45 AM Richard Kullmann < Richard.Kullmann.mpikg.mpg.de> wrote: > Hello again, > > I tried to run the test cases with my files. For that, I just replaced > the top and inpcrd files with my corresponding files (and commented out > the dacdif part). For GB, it ran through again without issue. For PB, I > got the same error as before. So maybe there is something wrong with my > files? What part could let GB run but not PB? > An important note might be that I created the top files for MMPBSA AFTER > I had already done the simulation, and I only added the PBRadii option > then. Furthermore I use tip5p, but that should not be relevant for > implicit solvent calculations, right? Finally I am also loading custom > parameters for special residues, but this has also not been a problem > before. > Does any of this give you an idea of whats going on? > Thank you very much again! > > Best regards, > > Richard > > On 4/5/22 20:42, Ray Luo wrote: > > Great! Could you next use an input file in one of the test cases that is > > closest to your own job without change and run your job again? Let's see > > what happens. > > > > 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 Tue, Apr 5, 2022 at 8:38 AM Richard Kullmann < > > Richard.Kullmann.mpikg.mpg.de> wrote: > > > >> Dear Ray, > >> > >> both GB and PB tests run without issues. > >> > >> Best, > >> > >> Richard > >> > >> > >> -------- Forwarded Message -------- > >> Subject: Re: [AMBER] MMPBSA.py PB calculation not working > >> Date: Tue, 5 Apr 2022 07:48:50 -0700 > >> From: Ray Luo <rluo.uci.edu> > >> To: Richard Kullmann <richard.kullmann.mpikg.mpg.de> > >> > >> > >> > >> Richard, > >> > >> Do you see any problem running mmpbsa.py tests under > >> $AMBERHOME/AmberTools/test/mmpbsa_py? > >> > >> All the best, > >> 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 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/amber > >> > > _______________________________________________ > > 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 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Apr 06 2022 - 10:30:03 PDT