On 08/07/2009 12:43 PM, Daniel Russel wrote:
Cool, so then option 2 can be: Use Charmm atom types as AtomType - pdb reader/writer translates to and from them using the topology file - they are unique and so can be used to index things
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.
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.
Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle