[AMBER] MMPBSA.py PB calculation not working

From: Richard Kullmann <Richard.Kullmann.mpikg.mpg.de>
Date: Mon, 4 Apr 2022 12:01:24 +0200

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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Received on Mon Apr 04 2022 - 03:30:03 PDT
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