Fixed bug reading PDB files with multiple locations for some atoms

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -121,7 +121,9 @@ class PDBFile(object):
         self._positions = []
         for model in pdb.iter_models(True):
             coords = []
-            for atom in model.iter_atoms():
+            for chain in model.iter_chains():
+                for residue in chain.iter_residues():
+                    for atom in residue.atoms:
                         pos = atom.get_position().value_in_unit(nanometers)
                         coords.append(Vec3(pos[0], pos[1], pos[2]))
             self._positions.append(coords*nanometers)