added 'NA' and 'CL' to set {'+', '-'} identifying ions
@@ -188,7 +188,9 @@ class Topography(object):
# Ions are all atoms of the solvent whose residue name show a charge.
return [i for i in self._solvent_atoms
if '-' in self._topology.atom(i).residue.name or
- '+' in self._topology.atom(i).residue.name]
+ '+' in self._topology.atom(i).residue.name or
+ 'NA' in self._topology.atom(i).residue.name or
+ 'CL' in self._topology.atom(i).residue.name]
def add_region(self, region_name, region_selection, subset=None):
"""
