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I have some problems with water and metals in binding site when using Autodock Vina.

Is it possible to make these flexible? They unfortunately remain where they are what leads to wrong interactions.

My other idea would be to delete it before docking, reinsert them and minimize everything.

Does anyone have a solution for metalloenzymes? (e.g. PDB:3NJY)

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For the water molecules, you can try hydrated ligand docking in which they are added in the ligand file. The documentation here: http://autodock.scripps.edu/resources/autodock-hydrated-docking. I am not sure if the same approach can be used for the metal atom.

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