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 [cid:cdf013bd-01d5-4d3d-9dd2-554c27674417]
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@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
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@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@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
participants (3)
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Elaine Meng -
Sowmya Indrakumar -
Sowmya Indrakumar