I think we need to make a list of what we want to be able to do with the
names. It seems like:
1) figure out which atoms are bonded to which other atoms
2) figure out how to set up a forcefield for the atoms
3) write a pdb file
4) write a mol2 file
5) allow one to figure out the element
what else?
The combination of the PDB name with the residue name containing allows
all of these (assuming we get the mapping right for mol2).
It sounds like Charmm by itself isn't enough to (3) at least (what about
(1)?). What about Mol2?