Custom Search
-- 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/amberReceived on Tue Apr 05 2022 - 12:00:03 PDT