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
> >>
> >> _______________________________________________
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> <http://lists.ambermd.org/mailman/listinfo/amber>
> >>
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Received on Tue Apr 05 2022 - 12:00:03 PDT