ValueError: invalid literal for int() with base 10: 'BOND'

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douaki ali

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Sep 12, 2022, 12:43:32 PM9/12/22
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I am getting the following error.

[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
  File "/home/ali/miniconda3/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 545, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 461, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/home/ali/miniconda3/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 748, in cleantop
    rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix())
  File "/home/ali/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/ali/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 337, in read
    self._parse_dihedrals(line, dihedral_types, proper_multiterm_dihedrals,
  File "/home/ali/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 582, in _parse_dihedrals
    i, j, k, l = [int(x)-1 for x in words[:4]]
  File "/home/ali/miniconda3/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 582, in <listcomp>
    i, j, k, l = [int(x)-1 for x in words[:4]]
ValueError: invalid literal for int() with base 10: 'BOND'
Exiting. All files have been retained.
complex.gro
topol.top
index.ndx
em.tpr
dop.itp
dop.prm
gmx_MMPBSA.log

douaki ali

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Sep 12, 2022, 12:44:12 PM9/12/22
to gmx_MMPBSA
please find attached 10 frames.
tra10frames.xtc

Mario Sergio Valdes

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Sep 12, 2022, 1:10:17 PM9/12/22
to gmx_MMPBSA
The trajectory has only 1417 atoms, while the complex has 1440. Please attach a valid trajectory file.
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