Probably but we might want to discuss changeing this in mdtraj in the future
On Feb 12, 2014 3:31 PM, "Christian Schwantes" <notifications@github.com>
wrote:

> In src/python/metrics/contact.py:
>
> > @@ -114,7 +114,7 @@ def prepare_trajectory(self, trajectory):
> >              residue_to_alpha = np.zeros(num_residues)  # zero based indexing
> >              for i in range(num_atoms):
> >                  if trajectory.topology.atom(i).name == 'CA':
> > -                    residue = trajectory.topology.residue(i).index - 1
> > +                    residue = trajectory.topology.atom(i).residue.index - 1
>
> one question though, should we *always* be subtracting one?
>
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