[Chimera-users] Chimera PDB2PQR

[Sowmya Indrakumar]

Hi Elaine,
Thanks a lot for your comments on this. 
I did try all that you mentioned. 

Finally, running the pqb2pqr locally on Linux to generate pqr worked fine. But running the same on windows did not work for me.

I used the generated pqr in chimera, that looks alright. 

I do not know what sure why it does not run properly on windows. Would be nice to get feedback on the same from the developers. 

Best,
Sowmya



Sent from my iPhone
> On 21 Feb 2019, at 20.54, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
>> 
>