Possible unsupported residue names in CHARMM (.rtf)

[rwxayheee]

The default templates have residue names and disambiguation based on Amber. This can be inconsistent with Gromacs or Schrodinger.

For example, RNA structure prepared from Schrodinger with older CHARMM force field (???) has A,U,C,G as RA,RU,RC,RG (source: https://userguide.mdanalysis.org/1.1.1/standard_selections.html). These will cause an error saying ligand does not exist and cannot be fetched from CCD.

These inconsistencies need some further investigation. Some useful configurations can be prepared for Amber, Gromacs, and Schrodinger. At the moment, it's possible to edit the ambiguous dict as a quick walkaround.

[rwxayheee]

fixed in #256