Traceback (most recent call last):
File "opt/anaconda3/envs/propka/bin/propka3", line 33, in <module>
sys.exit(load_entry_point('propka', 'console_scripts', 'propka3')())
File "propka/propka/run.py", line 42, in main
my_molecule = read_molecule_file(pdbfile, my_molecule)
File "propka/propka/input.py", line 113, in read_molecule_file
mol_container.extract_groups()
File "propka/propka/molecular_container.py", line 81, in extract_groups
self.conformations[name].extract_groups()
File "propka/propka/conformation_container.py", line 70, in extract_groups
self.setup_and_add_group(group)
File "propka/propka/conformation_container.py", line 165, in setup_and_add_group
self.init_group(group)
File "propka/propka/conformation_container.py", line 176, in init_group
group.setup()
File "propka/propka/group.py", line 321, in setup
self.setup_atoms()
File "propka/propka/group.py", line 744, in setup_atoms
PROTONATOR.protonate_atom(the_nitrogen[0])
IndexError: list index out of range
Running PROPKA on 1HCH gives the following error: