On 08/07/2009 01:06 PM, Daniel Russel wrote: > 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