[Chimera-users] change the protonation states

[Elaine Meng]

Hi Qchao,
There is no choice to make Lys and Arg uncharged, but after adding hydrogens, you can simply delete the specific hydrogens that you don't want from those residues to make them uncharged.

As for Asp, Glu (and His if you want to do that too) there are two general ways to do it in AddH:

(1) In the AddH dialog, there is a "Protonation states for:" menu.  In that menu you would choose "aspartic acid" and then below it, "Individually chosen," and then for each Asp that you want protonated, put a check mark on which sidechain oxygen you want to put the H on.  See image attached.  Then in the "Protonation states for:" menu, choose "glutamic acid" and "Individually chosen" and do the same thing for whichever Glu you want to make neutral.

- OR -

(2) text-edit your PDB input file to change residue names, so that the Glu you want neutral are named GLH and the Asp you want neutral are ASH.  Then open the edited file.  Then in the AddH dialog, under "Protonation states for: aspartic acid, glutamic acid" choose "Residue-name-based."

There are similar options with the "addh" command but I thought you may be using the AddH GUI, so that is what is described above.  For more details see AddH help:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>

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




> On Mar 23, 2022, at 8:15 PM, 孙钦超 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> I would like to make the Glu and Asp protonated, and the Lys and Arg uncharged.
> 
> While I was trying to do it by addH function with chosing the protonation sates option -> Asp, or chose His. The resulting protonation states of Glu and Arg were the same, as Glu deprotonated and Arg protonated.
> 
> How could I reach the right protonatation states as I expected?
> 
> Thanks 
> 
> Qchao
> 
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