Dear Ehud:
A quick google search turned up:
http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl
# A.A. BMRB SC PDB UCSF MSI XPLOR SYBYL* MIDAS*
DIANA
# ---- ---- ---- ---- ---- ---- ----- ----- -----
-----
G HA2 pro-R 1HA HA1 HA1 HA2 HA2
HA1
G HA3 pro-S 2HA HA2 HA2 HA1 HA1
HA2
So by PDB convention the pro-R hydrogen is 1HA and the pro-S hydrogen is 2HA.
But I would never trust any .gro or .pdb file. I have done this in the
past and have always just done a chirality calculation on the structure.
Chris.
-- original message --
Is there a convention about the chirality of the HA1 and HA2 hydrogen
atoms in Glycine (relative to the C-alpha)?
Glycine is non-chiral, but if one tries to mutate it to another L amino
acid, one of these hydrogens should be picked as the analog of a
sidechain. Which one is it?
As most PDB files do not contain hydrogens, this question seems to be
about the behavior of pdb2gmx when creating a .gro file with an all-atom
force field (such as opls-aa).
Thanks,
Ehud Schreiber.
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