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
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage