Hiiii all, I have doubts regarding the positioning of the docked conformers. I found that some conformers were far away from the active site and outside the grid box. Is it normal as some of the conformers gave good docking scores at the desired active site.
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I do not believe this is correct. You should not receive results that are outside of your search space. Are you running AutoDock or AutoDock Vina? If AutoDock, when you set the grid box does the visual box cover the appropriate area on the macromolecule. If the confirmation is falling outside the grid box or search space I would not proceed with any calculations and urge you to determine the cause.
My first guess would be that your grid box might be incorrectly set. AutoDock and AutoDock Vina have different parameters for the search space. Ensure that you are not confusing the two.
Undergraduate Researcher at Drexel University, Class of 2018
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