Re: [IMP-dev] Atom::create

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