Fix possible bug in `AmberPrmTopFile.createSystem()` (#3489)

* Only call set switching function/distance on nonbonded force(s)

* Also catch CustomNonbondedForce

* Fix logic around setEwaldErrorTolerance

wrappers/python/openmm/app/amberprmtopfile.py

@@ -290,9 +290,7 @@ class AmberPrmtopFile(object):
         for force in sys.getForces():
             if isinstance(force, mm.NonbondedForce):
                 force.setEwaldErrorTolerance(ewaldErrorTolerance)
-        if removeCMMotion:
-            sys.addForce(mm.CMMotionRemover())
-
+            if isinstance(force, (mm.NonbondedForce, mm.CustomNonbondedForce)):
                 if switchDistance and nonbondedMethod is not ff.NoCutoff:
                     # make sure it's legal
                     if (_strip_optunit(switchDistance, u.nanometer) >=
@@ -305,4 +303,7 @@ class AmberPrmtopFile(object):
                     force.setUseSwitchingFunction(True)
                     force.setSwitchingDistance(switchDistance)
 
+        if removeCMMotion:
+            sys.addForce(mm.CMMotionRemover())
+
         return sys