Add example on small molecule / protein MD from xtal structure about molecular-design-toolkit HOT 3 CLOSED

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 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

from molecular-design-toolkit.

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

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

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