fixes for python2 and forcefield class

wrappers/python/simtk/openmm/app/forcefield.py

@@ -2439,7 +2439,7 @@ class LennardJonesGenerator(object):
 
         for atom in data.atoms:
             self.force.addParticle((typeToMergedType[data.atomType[atom]],))
-        self.force.setUseLongRangeCorrection(True)
+        self.force.setUseLongRangeCorrection(bool(args.get('useLongRangeCorrection', False)))
         self.force.setCutoffDistance(nonbondedCutoff)
         sys.addForce(self.force)
 

wrappers/python/tests/TestCharmmFiles.py

@@ -285,13 +285,13 @@ class TestCharmmFiles(unittest.TestCase):
         for residue in psf.topology.residues():
             atoms = [atom.name for atom in residue.atoms()]
             if residue.name == "M14":
-                self.assertCountEqual(m14, atoms)
+                self.assertEqual(sorted(m14), sorted(atoms))
             elif residue.name == "TIP3":
-                self.assertCountEqual(tip3, atoms)
+                self.assertEqual(sorted(tip3), sorted(atoms))
             elif residue.name == "POT":
-                self.assertCountEqual(pot, atoms)
+                self.assertEqual(sorted(pot), sorted(atoms))
             elif residue.name == "CLA":
-                self.assertCountEqual(cla, atoms)
+                self.assertEqual(sorted(cla), sorted(atoms))
             else:
                 self.assertTrue(False)
 

wrappers/python/tests/systems/ions.pdb

 CRYST1   12.009   12.338   11.510  90.00  90.00  90.00 P 1
 ATOM      1  SOD SOD I   1      -5.844   1.432   3.239  1.00  0.00      ION NA
-ATOM      2  CLA CLA I   2      -5.605  -3.153   1.213  1.00  0.00      ION CL
+ATOM      2  CLA CLA I   2      -5.605  -1.153   1.213  1.00  0.00      ION CL
 END
\ No newline at end of file