On 08/07/2009 02:25 PM, Daniel Russel wrote:
Sure, but what we call the atom type isn't the atom type - it's the name.Sure it is. Why do you say it is not?
I think anybody that has used any other package will be rather confused that our atom "type" is what PDB calls the "name", and not the forcefield type, particularly given that we already have a particle attribute called "name". (I also have a problem with atoms that are clearly identical, such as benzene carbons, being labeled as different types.) This is why I propose we use the particle name for this purpose. To determine elements, forcefield types, etc. using the combination of the atom name and the residue name (as you appear to be proposing) certainly makes sense to me.
Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle