[Chimera-users] how to know the net charge of my system

Sara Luz Gomez Maya sara.gomezmaya at sns.it
Tue Jun 29 00:26:08 PDT 2021

Dear Elaine,

Thank you very much for your prompt reply. It helped me a lot.


On Mon, Jun 28, 2021 at 8:16 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Sara,
> You could get an estimate by using Add Charge, which requires using AddH
> first.  If you need commands they are simply
> addh
> addcharge
> ... and then look in the Reply Log (in menu under Favorites) for the net
> charge.
> However, Chimera does NOT do any detailed pKa predictions, and will assume
> that Asp, Glu are always negatively charged, and Lys, Arg always positively
> charged.  His (histidine) may vary depending on its local H-bonding
> pattern.  Also, if you have nonstandard residues like ligands, it may take
> longer (and sometimes fail) to calculate their charges.
> If you want a more careful estimate of the charge of a protein with pKa
> predictions, you may need to use some other program(s), e.g.
>   <https://server.poissonboltzmann.org/pdb2pqr>
>   <https://www.ddl.unimi.it/vegaol/propka.htm>
> H++
>   <http://biophysics.cs.vt.edu/>
> However, I don't remember if these servers report the net charge in a
> simple way or whether you'd have to add up the charges yourself to figure
> out it.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jun 28, 2021, at 2:28 AM, Sara Luz Gomez Maya via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear all,
> > I'd like to know if there is a way to know the net charge of a system
> when opening the pdb file with Chimera. If so, is it possible to do it by
> means of the command line?
> > Thanks in advance,
> > Sara
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