VMD-L Mailing List

From: Ernesto Aleksei Delgado Hurtado (erdelgado_at_udec.cl)
Date: Tue Feb 19 2019 - 12:17:23 CST

El 2019-02-19 11:44, 김민재 escribió:
> Hi all
>
> I am currently attempting to run a MD simulation on 1CA2, and I
> created a water box around carbonic anhydrase for a PME. When I used
> vmd to neutralize this system the program only added 2 Na+ ions. I was
> curious about why the system would only have a net charge of -2 since
> 1CA2 has 31 acidic and 41 basic residues.
> In case I got the number of acidic and basic residues wrong, is there
> a function in VMD that counts them for you?
>
> Thanks

Hi

You can count the number of acidic and basic residues by loading your
psf or pdb and running in the Tk Console
[atomselect top "acidic and alpha"] num
[atomselect top "basic and alpha"] num
respectively. But note that the charge of your system depends in the
protonation state of your residues too, and that depends on the pH. To
get the total charge of your system and convince yourself that the
charge is correct you can run in the Tk Console
eval vecadd [[atomselect top all] get charge]