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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Another no PQR file in outputs issue #337

Open lbizzio opened 1 year ago

lbizzio commented 1 year ago

Hello, I am using PDB2PQR on the web server at https://server.poissonboltzmann.org/. I uploaded the PDB file 5YCK obtained from the RCSB databank (https://www.rcsb.org/structure/5YCK). However, when I submit the job using default parameters for this file when it says 'Job completed' it only gives me back a couple of text file logs and no PQR file. Furthermore, I am blocked from using the button that says "Use results for APBS", indicating that there is indeed no usable output. When I look at the log files the only thing that looks suspicious is a segment that ends with the term "KeyError: 'R'". Could you please let me know why this tool seems not to be working? The PDB file comes straight from the most reputable curated source, so I figured that it should work fine and have no problems with it. The output files I did receive are attached to this message. Thank you very much.

pdb2pqr.stdout.txt ebmlyhhhjz.log pdb2pqr.stderr.txt

sobolevnrm commented 1 year ago

PDB2PQR does not have parameters for rubidium. Could you try removing the ion from the input PDB file and let us know if that solves the problem? Thanks.