> Note, however, my earlier point, so there is no room for confusion: > multiple atoms in a given residue can have the same atom type (e.g. > all the hydrogens may have the same type). The atom type does not > suffice to uniquely define the atom name - that's why you need a > separate atom name. And this would certainly need to be user- > settable if the user wants to make any novel molecules that don't > currently exist in the topology file/ligand database. I thought you said you could use the topology file to go from charmm atom types to pdb names? Or do you also need bonds or other non-type information? Which might be OK, but perhaps complicated.
> > The important distinction here is that atom names are just a > construct to make humans' lives easier, while atom types are what > the universe cares about. If a user wants to name an atom, they can just name the particle, so that is well solved.
The important thing is to have a minimal scheme for tagging atoms which supports something 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
Identifying atoms via their PDB names and the type of their parent as is currently sort of done, works fine.
So what is a minimal set of CHARMM-related information that can do what we need? Is it simpler/more useful than the PDB-based alternative?