Add a test case for the colinear lonepair facility in CHARMM psf parser.

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

@@ -714,6 +714,7 @@ class CharmmPsfFile(object):
             if atom.type is not None:
                 # This is the most reliable way of determining the element
                 atomic_num = atom.type.atomic_number
+                if atomic_num != 0:
                     elem = element.Element.getByAtomicNumber(atomic_num)
             else:
                 # Figure it out from the mass
@@ -911,6 +912,7 @@ class CharmmPsfFile(object):
                                          bond.bond_type.req*length_conv)
 
         # Add virtual sites
+        if hasattr(self, 'lonepair_list'):
             if verbose: print('Adding lonepairs...')
             for lpsite in self.lonepair_list:
                 index=lpsite[0]

wrappers/python/tests/TestCharmmFiles.py

@@ -141,17 +141,20 @@ class TestCharmmFiles(unittest.TestCase):
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
         psf = CharmmPsfFile('systems/chlb_cgenff.psf')
         crd = CharmmCrdFile('systems/chlb_cgenff.crd')
-        # move the position of the lonepair on Cholride
-        params = CharmmParameterSet('systems/par_all36_cgenff.prm',
-                                    'systems/top_all36_cgenff.rtf')
-        # Box dimensions (found from bounding box)
+        params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
+                                    'systems/par_all36_cgenff.prm')
         plat = Platform.getPlatformByName('Reference')
-        system = psf.createSystem(params, nonbondedMethod=PME,
-                                  nonbondedCutoff=8*angstroms)
-
+        system = psf.createSystem(params)
         con = Context(system, VerletIntegrator(2*femtoseconds), plat)
         con.setPositions(crd.positions)
+        init_coor = con.getState(getPositions=True).getPositions()
+        # move the position of the lonepair and recompute its coordinates
+        crd.positions[12] = Vec3(0.5, 1.0, 1.5) * angstrom
+        con.setPositions(crd.positions)
+        con.computeVirtualSites()
+        new_coor = con.getState(getPositions=True).getPositions()
         
+        self.assertEqual(init_coor, new_coor)
 
     def test_InsCode(self):
         """ Test the parsing of PSF files that contain insertion codes in their residue numbers """