[Chimera-users] AddH on N atom in N-terminal

[Elaine Meng]

Just based on chemistry... the pKa of the N-terminal nitrogen will of course be different for different proteins, but a rough estimate is that the N-terminal free amine (not in a peptide bond) has a pKa of approximately 8, meaning it will be mostly positively charged at neutral pH (7).

You can delete one H if you want to.  Or, you can change the atom type of that atom from N3+ to N3 before using addh.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 16, 2021, at 12:43 AM, 陈恩博 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello.
> When I use addH to add H atoms on N atom in N-terminal of Peptide chain, I find 3 H were added on this N.
> Why the addH result is C-NH3 and not C-NH2?
> Thanks!