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PDBQT is not a standard molecular structure format. The scoring function has changed since the tutorial was recorded, but only in the part that is independent of the conformation: the ligand-specific penalty for flexibility has changed. My docked conformation is the same, but my energies are different from what you get in the video tutorial. Note that the probability of failing to find the mininum may be different with a different system. Even though with this receptor-ligand pair, the minimum of the scoring function corresponds to the correct conformation, the docking algorithm sometimes fails to find it. The docking algorithm is non-deterministic. Why is my docked conformation different from what you get in the video tutorial? Your Linux cluster is configured in such a way as to disallow spawning threads. Vina runs well on my machine, but when I run it on my exotic Linux cluster, I get a “boost thread resource” error. The command line options changed somewhat since the tutorial has been recorded. The goal of 8 Ball Pool is to have no more than two balls remaining at the end of the game. They are given three more shots and must land it in a pocket to continue playing. The game begins when the player takes their first shot at the cue ball. |
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