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 topology file is used to map PDB atom name to CHARMM atom types. You
can't easily go the other way, since an atom type is basically just the
element and some rough categorization of the electronic environment
(e.g. aromatic, sp2, sp3 etc.). For example, in benzene all 6 carbons
will have the same type (they are sterically and electronically
identical, of course), but they'll have different atom names. In
principle you can determine the atom name from the topology, but in
general it's far easier just to store that name in the particle,
particularly once you start modifying the topology (mutating residues,
adding/removing sidechains, etc.).
Identifying atoms via their PDB names and the type of their parent as is
currently sort of done, works fine.
Sure, but what we call the atom type isn't the atom type - it's the
name. It would make more sense to use the particle name for that
purpose, therefore, and put real type information (e.g. CHARMM or Mol2
atom type name, element) in a "real" AtomType.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle