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

陈恩博 chenenbo at pku.edu.cn
Thu Jun 17 00:01:21 PDT 2021


> -----Original Messages-----
> From: "Elaine Meng" <meng at cgl.ucsf.edu>
> Sent Time: 2021-06-16 23:00:28 (Wednesday)
> To: "陈恩博" <chenenbo at pku.edu.cn>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] AddH on N atom in N-terminal
> 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
> -----
> 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!

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