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.