Fixed error leading to duplicate bonds (#228)

openmm · Sep 9, 2021 · 9dc7681 · 9dc7681
1 parent 80bd5b9
commit 9dc7681
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pdbfixer/pdbfixer.py b/pdbfixer/pdbfixer.py
@@ -917,7 +917,7 @@ def addMissingAtoms(self, seed=None):
             # Add the new bonds to the original Topology.
 
             inverseAtomMap = dict((y,x) for (x,y) in existingAtomMap.items())
-            for atom1, atom2 in newTopology.bonds():
+            for atom1, atom2 in newBonds:
                 self.topology.addBond(inverseAtomMap[atom1], inverseAtomMap[atom2])
         else: