diff --git a/parmed/openmm/topsystem.py b/parmed/openmm/topsystem.py
index 923865bc19e5001ac2540af53384ef951f170801..5a5b363f1530f45caf56615667ffd2948a6ba635 100644
--- a/parmed/openmm/topsystem.py
+++ b/parmed/openmm/topsystem.py
@@ -392,10 +392,12 @@ def _process_nonbonded(struct, force):
     bond_graph_exceptions = defaultdict(set)
     for atom in struct.atoms:
         for a2 in atom.bond_partners:
-            bond_graph_exceptions[atom].add(a2)
+            if atom is not a2:
+                bond_graph_exceptions[atom].add(a2)
             for a3 in a2.bond_partners:
                 if a3 is atom: continue
-                bond_graph_exceptions[atom].add(a3)
+                if atom is not a3:
+                    bond_graph_exceptions[atom].add(a3)
 
     # TODO should we compress exception types?
     for ii in range(force.getNumExceptions()):