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@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!