Fix error message formatting related to bonds to extra sites (#5065)

wrappers/python/openmm/app/forcefield.py

@@ -1888,8 +1888,8 @@ def _findMatchErrors(forcefield, res):
 
     def formatBondDiff(key, diff):
         """Formats a string describing elements associated with a different number of bonds."""
-        name1 = elem.Element.getByAtomicNumber(key[0]).symbol if key else 'extra site'
-        name2 = elem.Element.getByAtomicNumber(key[1]).symbol if key else 'extra site'
+        name1 = elem.Element.getByAtomicNumber(key[0]).symbol if key[0] else 'extra site'
+        name2 = elem.Element.getByAtomicNumber(key[1]).symbol if key[1] else 'extra site'
         return f'{name1}-{name2} bond' + ('' if diff == 1 else 's')
 
     def pickBestMatch(bestMatches):

wrappers/python/tests/TestForceField.py

@@ -987,6 +987,18 @@ class TestForceField(unittest.TestCase):
         with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The force field contains no residue templates'):
             makeSystem(pdbLines)
 
+        # Make water with an extra site and an (invalid) bond to it.
+        pdbLines = [
+            'ATOM      0 O    HOH A   1       0       0       0                           O',
+            'ATOM      1 H1   HOH A   1       0       0       0                           H',
+            'ATOM      2 H2   HOH A   1       0       0       0                           H',
+            'ATOM      3 M    HOH A   1       0       0       0                          EP',
+            'CONECT    0    3'
+        ]
+        forcefield = ForceField('opc.xml')
+        with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The set of atoms matches HOH, but the residue has 1 extra site-O bond too many'):
+            makeSystem(pdbLines)
+
     def test_Wildcard(self):
         """Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in the ffxml are correctly registered"""