Fixing systembuilder [WIP]

I've made some good headway in getting systembuilder fixed, but now run into a problem with GB parameters for the ligand:
```
Traceback (most recent call last):
  File "tests/test_alchemy.py", line 578, in <module>
    test_systembuilder_lysozyme_pdb_mol2()
  File "tests/test_alchemy.py", line 533, in test_systembuilder_lysozyme_pdb_mol2
    print "%s has %d particles" % (name, thing.system.getNumParticles())
  File "/Users/choderaj/code/yank/install/lib/python2.7/site-packages/yank-0.9.0-py2.7.egg/yank/systembuilder.py", line 176, in system
    self._create_system()
  File "/Users/choderaj/code/yank/install/lib/python2.7/site-packages/yank-0.9.0-py2.7.egg/yank/systembuilder.py", line 164, in _create_system
    self._system = forcefield.createSystem(self._topology, **self.system_creation_parameters)
  File "/Users/choderaj/code/yank/install/lib/python2.7/site-packages/simtk/openmm/app/forcefield.py", line 507, in createSystem
    force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
  File "/Users/choderaj/code/yank/install/lib/python2.7/site-packages/simtk/openmm/app/forcefield.py", line 1245, in createForce
    raise ValueError('No GBSAOBC parameters defined for atom type '+t)
ValueError: No GBSAOBC parameters defined for atom type MOL-C1
```