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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 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.
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
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