Fix two issues with virtual site handling: (#4812)

* In CharmmPsfFile, add lonepair exceptions even when no Drude particles
  are present

* In ForceField, correctly update the indices of virtual site exclusion
  reference particles in a residue when applying a patch to it

wrappers/python/openmm/app/charmmpsffile.py

@@ -1410,12 +1410,12 @@ class CharmmPsfFile(object):
                 idxa = pair[1]
                 parent_exclude_list[idx].append(idxa)
                 force.addException(idx, idxa, 0.0, 0.1, 0.0)
-            # If lonepairs and Drude particles are bonded to the same parent atom, add exception
-            for excludeterm in parent_exclude_list:
-                if(len(excludeterm) >= 2):
-                    for i in range(len(excludeterm)):
-                        for j in range(i):
-                            force.addException(excludeterm[j], excludeterm[i], 0.0, 0.1, 0.0)
+        # If lonepairs and Drude particles are bonded to the same parent atom, add exception
+        for excludeterm in parent_exclude_list:
+            if(len(excludeterm) >= 2):
+                for i in range(len(excludeterm)):
+                    for j in range(i):
+                        force.addException(excludeterm[j], excludeterm[i], 0.0, 0.1, 0.0)
         # Exclude 1-2 and 1-3 pairs as well as the lonepair/Drude attached onto them
         if nbxmod > 1:
             for ia1, ia2 in self.pair_12_list:

wrappers/python/openmm/app/forcefield.py

@@ -871,6 +871,7 @@ class ForceField(object):
                         newSite = deepcopy(site)
                         newSite.index = indexMap[site.index]
                         newSite.atoms = [indexMap[i] for i in site.atoms]
+                        newSite.excludeWith = indexMap[site.excludeWith]
                         newTemplate.virtualSites.append(newSite)
 
                 # Build the lists of bonds and external bonds.