Fails to make a universe from 4BXW.pdb

[kaceyaurum]

When a universe should be created, a ZeroDivisionError is raised.

---

ZeroDivisionError Traceback (most recent call last)
in ()
----> 1 mda.Universe(path + '4BXW.pdb')

/usr/local/lib/python2.7/dist-packages/MDAnalysis/core/AtomGroup.pyc in init(self, _args, *_kwargs)
4337 try:
4338 with parser(self.filename, universe=self) as p:
-> 4339 self._topology = p.parse()
4340 except IOError as err:
4341 raise IOError("Failed to load from the topology file {0}"

/usr/local/lib/python2.7/dist-packages/MDAnalysis/topology/PDBParser.pyc in parse(self)
88 structure['atoms'] = atoms
89
---> 90 bonds = self._parsebonds(atoms)
91 structure['bonds'] = bonds
92

/usr/local/lib/python2.7/dist-packages/MDAnalysis/topology/PDBParser.pyc in _parsebonds(self, atoms)
179 lines = (line for line in f if line[:6] == "CONECT")
180 for line in lines:
--> 181 atom, atoms = _parse_conect(line.strip())
182 for a in atoms:
183 bond = tuple([mapping[atom], mapping[a]])

/usr/local/lib/python2.7/dist-packages/MDAnalysis/topology/PDBParser.pyc in _parse_conect(conect)
211 atom_id = np.int(conect[6:11])
212 n_bond_atoms = len(conect[11:]) // 5
--> 213 if len(conect[11:]) % n_bond_atoms != 0:
214 raise RuntimeError("Bond atoms aren't aligned proberly for CONECT "
215 "record: {}".format(conect))

ZeroDivisionError: integer division or modulo by zero

import MDAnalysis as mda

u = mda.Universe('4BXW.pdb')

[richardjgowers]

This one is caused by a CONECT record which only lists one number (CONECT 2727), which as far as I understand means nothing? So I guess a small check to make sure that CONECT lines with only one record get ignored?

[jbarnoud]

Closed by #949