[Chimera-users] Chimera PDB2PQR

[Elaine Meng]

Hi Sowmya,
This calculation is not done inside of Chimera but at a webserver run by another group:

<http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/>

So reinstalling Chimera would not be expected to have any effect on this.

You could try running that webservice directly from the link above, but it will probably give the same results.  I also saw this behavior even when I tried pH 1 and 12, which I would expect to give some difference, and even when I used the newer version of that webserver:

<http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/>

I don’t know why there is no change in the total charge. However, it might change if you choose a different forcefield (e.g. AMBER instead of PARSE), but I did not try that.  Maybe PARSE doesn’t include hydrogens.

You could try using a different force field, and if that doesn’t help, maybe ask your question on the pdb2pqr-users mailing list (link at the bottom of the webserver page).

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

> On Feb 21, 2019, at 1:44 AM, Sowmya Indrakumar <soemya at kemi.dtu.dk> wrote:
> 
> Dear Developers,
> I am try to use Chmiera for electrostatic calculations. I first make the PQR file using the PDB2PQR at different pH, however I do not see a change in the total charge, the REMARK section shows that total charge is 1 always. I'm using the default setting as shown in the attached screenshot. Please let me know what might be going wrong? I installed the new version twice.
> Thanks a lot for your help!
> Regards
> Sowmya
>