Im preparing protein using autodock for docking in vina. But during the step of repairing missing atom, some error came (a python shell) and that step is not running.I repaired my protein structure in Chimera using the Dock Prep tool to ensure that all missing atoms and incomplete side chains (such as Thr722, which was part of the active site) were properly rebuilt. In this step, I also deleted water molecules and added hydrogens so that the missing atoms could be modeled correctly. I then saved the repaired structure as a new PDB file. Next, I imported this file into AutoDockTools (ADT) to finalize the receptor preparation for docking in AutoDock Vina. In ADT, I added polar hydrogens and Kollman charges, which are required for docking calculations, and saved the protein in the PDBQT format. Is this workflow correct?
