support gen-pairs=no in Gromacs

This was actually fully supported already, since it parsed pairtypes and
assigned the exception parameters correctly from there. All this does is throw
an exception when pair parameters are not defined and gen-pairs=no.

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

@@ -264,7 +264,7 @@ class GromacsTopFile(object):
         if fields[1] != '2':
             raise ValueError('Unsupported combination rule: '+fields[1])
         if fields[2].lower() == 'no':
-            raise ValueError('gen_pairs=no is not supported')
+            self._genpairs = False
         self._defaults = fields
 
     def _processMoleculeType(self, line):
@@ -452,6 +452,7 @@ class GromacsTopFile(object):
         # constraint distances and exclusions.
         self._defines = OrderedDict()
         self._defines['FLEXIBLE'] = True
+        self._genpairs = True
         if defines is not None:
             for define, value in defines.iteritems():
                 self._defines[define] = value
@@ -822,6 +823,9 @@ class GromacsTopFile(object):
                         params = self._pairTypes[types][3:5]
                     elif types[::-1] in self._pairTypes:
                         params = self._pairTypes[types[::-1]][3:5]
+                    elif not self._genpairs:
+                        raise ValueError('No pair parameters defined for atom '
+                                         'types %s and gen-pairs is "no"' % types)
                     else:
                         continue # We'll use the automatically generated parameters
                     atom1params = nb.getParticleParameters(baseAtomIndex+atoms[0])