19 January 2024 1 7K Report

I am doing md simulation of HDAC11 protein with prospective ligands. I have completed molecular dynamics production run. But whenever I am doing MMPBSA.py assay, it is showing following error:

Loading and checking parameter files for compatibility...

cpptraj found! Using /home/mohon/anaconda3/envs/amber/bin/cpptraj

mmpbsa_py_energy found! Using /home/mohon/anaconda3/envs/amber/bin/mmpbsa_py_energy

Preparing trajectories for simulation...

100 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/mohon/anaconda3/envs/amber/bin/mmpbsa_py_energy

  calculating complex contribution...

  calculating receptor contribution...

  calculating ligand contribution...

Beginning PB calculations with /home/mohon/anaconda3/envs/amber/bin/mmpbsa_py_energy

  calculating complex contribution...

  File "/home/mohon/amber22/bin/MMPBSA.py", line 100, in

    app.run_mmpbsa()

  File "/home/mohon/amber22/lib/python3.11/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

  File "/home/mohon/amber22/lib/python3.11/site-packages/MMPBSA_mods/calculation.py", line 82, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

  File "/home/mohon/amber22/lib/python3.11/site-packages/MMPBSA_mods/calculation.py", line 472, in run

    error_list = [s.strip() for s in out.split('\n')

                                    ^^^^^^^^^^^^^^^

TypeError: a bytes-like object is required, not 'str'

Fatal Error!

All files have been retained for your error investigation:

You should begin by examining the output files of the first failed calculation.

Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the

manual for file naming conventions.

My input file configuration is given bellow:

Input file for running PB and GB

&general

   endframe=1000, verbose=2,

#  entropy=1,

/

&gb

  igb=2, saltcon=0.100

/

&pb

  istrng=0.100,

/Can any one help me with it ?

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