openmm/openmm-forcefields: Fix GAFF AM1-BCC charging bug for some molecules

When using the OpenEye toolkit, some molecules failed to charge with GAFF. See https://github.com/openforcefield/openforcefield/issues/492 Removed most perses_jacs_systems, updating the remaining ones with inputs used in AMBER-TI publication, https://pubs.acs.org/doi/10.1021/acs.jcim.9b00105 Fix a bug where some molecules with pyramidal atoms would cause exceptions when read from cach