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 ?