Dear Amber Community,
I’m trying to use the gromber utility in ParMed, but I am getting the below error message. Can you please help me troubleshoot and resolve this issue?
gromber ligand.top ligand.gro
Converting Gromacs topology peridinina.top to Amber. Using topology directory [/usr/local/gromacs/share/gromacs/top]. Getting coordinates (and box) from peridinin.pdb.
Unexpected failure:
ZeroDivisionError: float division by zero
Traceback is
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/tools/parmed_cmd.py", line 161, in _normaldo
action.execute()
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/tools/actions.py", line 4357, in execute
top = gromacs.GromacsTopologyFile(self.topfile,defines=self.defines)
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
self.read(fname, defines, parametrize)
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 337, in read
self._parse_dihedrals(line, dihedral_types, proper_multiterm_dihedrals,
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 585, in _parse_dihedrals
dih, diht = self._process_normal_dihedral(words, molecule.atoms, i,
File "/opt/anaconda3/envs/AmberTools20/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 883, in _process_normal_dihedral
scee=1/self.defaults.fudgeQQ,
Best,
Matthew
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Received on Sun Aug 22 2021 - 08:30:02 PDT
