UnicodeDecodeError: 'utf-8' codec can't decode byte 0x9d in position 2506: invalid start byte

[John Christian de Guzman]

I encountered the following error when running gmx_MMPBSA. Apparently there is not much information available online regarding this issue so I don't know exactly what went wrong and how to resolve it. Please help

INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ct md_final.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -nogui

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/ward.banico/.conda/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/ward.banico/.conda/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/ward.banico/.conda/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/ward.banico/.conda/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/ward.banico/.conda/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
tets
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 798, in cleantop
    for line in topf:
  File "/home/ward.banico/.conda/envs/gmxMMPBSA/lib/python3.9/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x9d in position 2506: invalid start byte
Exiting. All files have been retained.

[Mario Sergio Valdes]

Please, check if the topology file has non-ASCII character