Your ligand or receptor might not have been correctly protonated.If you are coming from AutoDock 4, a very common mistake is to specify the search space in 'points' (0.375 Angstrom), instead of Angstroms.Since the individual runs are executed in parallel, where appropriate, exhaustiveness also limits the parallelism.Unlike in AutoDock 4, in AutoDock Vina, each run can produce several results: promising intermediate results are remembered.These are merged, refined, clustered and sorted automatically to produce the final result. However, the number of runs is set by the exhaustiveness parameter. Each local optimization involves many evaluations of the scoring function as well asits derivatives in the position-orientation-torsions coordinates.The number of evaluations in a local optimization is guided by convergence and other criteria.The number of steps in a run is determined heuristically, depending on the size and flexibility of the ligand and the flexible side chains. Each step involves a random perturbation of the conformation followedby a local optimization (using the Broyden-Fletcher-Goldfarb-Shanno algorithm) and a selection in which the step is either accepted or not. ![]() ![]() In the current implementation, the docking calculation consists of a number of independent runs, starting from random conformations.Each of these runs consists of a number of sequential steps.
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