Add example on small molecule / protein MD from xtal structure

[avirshup]

Notebook shows how to get from crystal structure 3AID to implicit solvent dynamics with gasteiger partial charges (for speed only)

[avirshup]

This is currently blocked by my inability to get openbabel to report formal charges as anything other than 0 (there's a quaternary nitrogen in the current workflow that should have formal charge +1 and thus give the molecule a total charge of +1. However, OpenBabel does report that the nitrogen's atom type is 'N3+', so it clearly knows that it should be a cation.

Workarounds are:

• integrate RDKit, which will probably work better RDKit doesn't currently handle this, see Handling of non-standard or variable valency, like tetra-valent Nitrogen? rdkit/rdkit#358
• Continue to bang head against openbabel
• parse openbabel type string to look for pluses and minuses
• Use VSEPR to figure it out ourselves
• Switch to a different molecule (doesn't solve the problem)

EDIT: Basic fix added in #72

[avirshup]

Next incipient bug: OpenBabel PDB fields lack TER records, which makes them incompatible with antechamber in certain cases. See #74

[avirshup]

Added an initial version. May add an analysis section later, but the basic ligand simulation functionality is there.