Don't print volume and density for implicit solvent calculations... duh.
Change the cutoff to 10 Angstroms.
Put in disclaimers about using an up-to-date force field and give a link to
MacKerell's site.
Remove the RTF file. Thanks to changes in CHARMM 36, the atom types no longer
have to be parsed from RTF files and the PAR file we have is enough.
Furthermore, omitting that file here will make it difficult for people to use
the files provided here to simulate their system (which is a Good Thing -- they
should make sure they are using the latest parameters for that).
Do not choke on Amoeba-style topology files that do not have all of the
parameter types defined (small systems may not have torsions, tortors, or other
many-body terms.
Adjust CHARMM parameters to a 12 angstrom cutoff with a switch at 10 angstroms.

From all appearances that is the standard CHARMM force field.
A few small bug fixes and add a Restart file to the CHARMM OpenMM class list.
Sphinx files added via:

    sphinx-quickstart
        ['y' to autodoc, intersphinx, ifconfig, viewcode]
    sphinx-apidoc -P -o. chemistry
Updates to the sphinx input files to remove some of the classes that users don't
need to know about.
Remove documentation from bits that should not be documented.