[gmx-users] HA1/HA2 chirality of GLY

[chris.neale at utoronto.ca]

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.