[gmx-users] HA1/HA2 chirality of GLY

Ehud Schreiber schreib at compugen.co.il
Sun Jul 11 14:54:58 CEST 2010

Dear GROMACS users,


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).



Ehud Schreiber.


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