Dear Amber community,
I am using MMPBSA.py of AmberTools20 to calculate the binding energy in a
protein-ligand system. I get the following error:
*Beginning PB calculations with /home/chem/AmberTools20/amber20/bin/sander*
* calculating complex contribution... File
"/home/chem/AmberTools20/amber20/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa() File
"/home/chem/AmberTools20/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File
"/home/chem/AmberTools20/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File
"/home/chem/AmberTools20/amber20/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.*
For the same system and the same topology files, I get the same error with
AmberTools20 on two machines with Ubuntu and Centos. I get the the
following similar error with AmberTools18 on a different machine:
*Beginning PB calculations with
/cm/shared/apps/scientific/AMBER/amber18/bin/sander*
* calculating complex contribution... File
"/cm/shared/apps/scientific/AMBER/amber18/bin/MMPBSA.py", line 100, in
<module> app.run_mmpbsa() File
"/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File
"/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File
"/cm/shared/apps/scientific/AMBER/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 433, in run self.prmtop) + '\n\t'.join(error_list) +
'\n')CalcError: /cm/shared/apps/scientific/AMBER/amber18/bin/sander failed
with prmtop ../complex.parm7!*
Here is my mmpbsa.in script:
*&general startframe=1, endframe=5, interval=1,
receptor_mask=":1-130", ligand_mask=":131", strip_mask=".2121-56249",
verbose=1, keep_files=1, netcdf=1,/&pb istrng=0.15, /&decomp
idecomp=1, print_res="36,131", dec_verbose=1,/*
I run it with:
MMPBSA.py -O -i mmpbsa.in -o mmpbsa.out -do decomp.csv -sp full.parm7 -cp
complex.parm7 -rp rec.parm7 -lp lig.parm7 -y traj_1.nc
I prepared the prmtop files with:
ante-MMPBSA.py -p full.parm7 -r rec.parm7 -l lig.parm7 -c complex.parm7 -s
.2121-56249 -m :1-130 --radii mbondi2
I checked all parm7 files that I used above and the number of atoms match
with what I expect as ligand, receptor, complex and colvated systems.
I found a similar thread from 2018 in which a similar problem has been
reported but found no answer for it:
http://archive.ambermd.org/201804/0329.html
Other system details: Protein with 130 residues and a negatively-charged
ligand with 78 atoms. Total of 56249 atoms including OPC water, and ions in
the solvated system.
Could you please help me figure out the problem with this calculation?
Thanks,
Hamed S. Hayatshahi
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Received on Thu Oct 01 2020 - 14:00:04 PDT
