by jmeans » Wed Feb 24, 2016 2:29 pm
Sargis,
Yesterday after I made my initial post, I continued to troubleshoot the problem. My students are working on two different computational projects - one involving an RNA target and the other involving a protein target. They are docking different ligands with each of these targets. We were consistently getting the posted error with the RNA target with its group of ligands. I tried docking ligands from the protein project with the RNA and still got the same error. I tried running the protein target with some of its ligands, and I did not get that error; the docking results were displayed as expected. Also, I never got this error when using the Vina Wizard; I only got it with the AutoDock Wizard. Additionally, all of these files had been successfully docked with version 0.9 of PyRx on Fedora 20. I pulled two random RNA structures and one random protein structure from the PDB site. I got the same error running dockings with any of our ligands and all three of these random structures. Each time, I would have to restart Python Prescription, so the program was being restarted each time. This morning, I came in to continue troubleshooting, and I ran the update as you requested. I ran two docking jobs with the RNA target and ligands that had produced the error yesterday. I did not get the error on either job; they both posted the docking results as expected. I don't know if running the update ended up taking care of it, or if restarting the computer had done it. I shut it down yesterday before I left. I don't know if my student had shut down the machine at all since she started seeing these errors. Either way, it seems to be taken care of at this point. If the error rears its head again, I'll certainly follow your post to get the necessary info for you to troubleshoot it further.
Thank you.