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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 04 2022 - 03:30:03 PDT
