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. Why do I get “usage errors” when I try to follow the video tutorial? You can use ls or dir commands on Linux/MacOS and Windows, respectively, to list the contents of your directory. If you are referring simply to conf.txt in the command line, make sure you are in the same directory (folder) as this file. You should also make sure that the file path you are providing is correct with respect to the directory (folder) you are in, e.g. This setting can be changed in the control panel or system preferences. Oftentimes, file browsers hide the file extension, so while you think you have a file “conf.txt”, it’s actually called “”. Why do I get “can not open conf.txt” error? The file exists! By design, modern 64-bit machines can run 32-bit binaries natively. There are better programs for protein-protein docking. You might be able to do that, but AutoDock Vina is designed only for receptor-ligand docking. It can also be used for viewing the results.Ĭan I dock two proteins with AutoDock Vina? #Pymol tutorial hide show chain softwareWhat is the difference between AutoDock Vina and AutoDock Tools?ĪutoDock Tools is a module within the MGL Tools software package specifically for generating input (PDBQT files) for AutoDock or Vina. This is due to the fact that the scoring functions are different, and both are inexact. However, for any given target, either program may provide a better result, even though AutoDock Vina is more likely to do so. The performance was compared in the original publication, and on average, AutoDock Vina did considerably better, both in speed and accuracy. However, the source code, the scoring funcion and the actual algorithms used are brand new, so it’s more correct to think of AutoDock Vina as a new “generation” rather than “version” of AutoDock. It also uses the same type of structure format (PDBQT) for maximum compatibility with auxiliary software. AutoDock Vina inherits some of the ideas and approaches of AutoDock 4, such as treating docking as a stochastic global opimization of the scoring function, precalculating grid maps (Vina does that internally), and some other implementation tricks, such as precalculating the interaction between every atom type pair at every distance. What is the difference between AutoDock Vina and AutoDock 4?ĪutoDock 4 (and previous versions) and AutoDock Vina were both developed in the Molecular Graphics Lab at The Scripps Research Institute. While evaluating any docking engine in a retrospective virtual screen, it might make sense to select decoys of similar size, and perhaps other physical characteristics, to your known actives. The predictive accuracy varies a lot depending on the target, so it makes sense to evaluate AutoDock Vina against your particular target first, if you have known actives, or a bound native ligand structure, before ordering compounds.
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