Fix mol2 warnings

```
rmcgibbo@dn0a230977 ~/projects/mdtraj
$ PYTHONWARNINGS=error nosetests MDTraj/tests/test_mol2.py
...S..
----------------------------------------------------------------------
Ran 6 tests in 0.077s

OK (SKIP=1)
```
This is the key line that fixes the `SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame.` reported by @jchodera in #506