Zhiqiang Ye wrote: > I have question about the hydrogen atom name after building the > all-atom model. After building the all-atom model, the hydrogen name > "HA" means hydrogen bonded to C-alpha, but GLY has two HA, one is 1HA, > the other is 2HA. Which one is correponding to the sidechain in > other residue types? I checked several GLY in my model, I find always > it is 2HA that is corresponding to the side chain of other residue > type. Is this the standard criteria, or just modeller's choice?
Modeller uses IUPAC names for the atoms. It is indeed 2HA which corresponds to the side chain; see modlib/top.lib.
Ben Webb, Modeller Caretaker