Re: [AMBER] MMPBSA.py PB calculation not working

From: Ray Luo <rluo.uci.edu> Date: Mon, 4 Apr 2022 08:33:16 -0700

--
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> 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 -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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