Raise exception when processing Gromacs molecule with virtual sites

Virtual sites are never created by the OpenMM system, and their information is
not parsed from the Gromacs topology file. For now just throw an exception
rather than let them run, since TIP4Pew behaves *very* strangely...

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

@@ -114,6 +114,7 @@ class GromacsTopFile(object):
             self.exclusions = []
             self.pairs = []
             self.cmaps = []
+            self.has_virtual_sites = False
 
     def _processFile(self, file):
         append = ''
@@ -247,6 +248,11 @@ class GromacsTopFile(object):
                 self._processPairType(line)
             elif self._currentCategory == 'cmaptypes':
                 self._processCmapType(line)
+            elif self._currentCategory.startswith('virtual_sites'):
+                if self._currentMoleculeType is None:
+                    raise ValueError('Found %s before [ moleculetype ]' %
+                                     self._currentCategory)
+                self._currentMoleculeType.has_virtual_sites = True
 
     def _processDefaults(self, line):
         """Process the [ defaults ] line."""
@@ -483,6 +489,8 @@ class GromacsTopFile(object):
             if moleculeName not in self._moleculeTypes:
                 raise ValueError("Unknown molecule type: "+moleculeName)
             moleculeType = self._moleculeTypes[moleculeName]
+            if moleculeCount > 0 and moleculeType.has_virtual_sites:
+                raise ValueError('Virtual sites not yet supported by Gromacs parsers')
 
             # Create the specified number of molecules of this type.