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
On Aug 7, 2009, at 12:39 PM, Ben Webb wrote:
> On 08/07/2009 12:36 PM, Daniel Russel wrote: >> 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? > > The topology file maps CHARMM atom types to PDB atom names, and > defines the connectivity for each residue type. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev