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/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.