Answer for Why are the hetatoms removed from the protein PDB file before docking?

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The structure we are using is a crystal structure complexed with ligand(s), therefore, to dock the desired ligand with the protein in that particular position we need to remove the bound ligand by removing hetatoms from the PDB file. Sometimes, if we want to study the interactions of a ligand with the protein in the presence of the other one (already bound to the protein), then, in that case, we do not remove hetatoms from the protein.