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?
It is reasonable for a Charmm force field setup code to assign Charmm atom types to accelerate its runtime looking of scoring functions.
> > To avoid confusing our users we should probably not refer to "PDB > atom types" anywhere, because what you are calling an atom type is > really an atom name. perhaps, although we tend to use name to mean "user setable-string" which it definitely is not.