I'm docking an enzyme by using maestro, there is an metal locate at the docking active site, I have already tried a few methods but there are still show the metal is interact with ligands in glide result.
Firstly, open your target enzyme on the workspace and go to the structural hierarchy click on the enzyme and expand then it will appear ligand, protein chain, solvent, and one more option ie other. So, you will expand other and it will show metals or ions available in the enzyme so select and delete.
If your protein is a metalloenzyme with a metal in the active site, it would be expected to interact with a ligand that is a substrate or active-site inhibitor of the enzyme.
I agree with Dr. Rudy J Richardson, but if you have another purpose and still want to prevent bonding with metal atoms, you can use the ‘Excluded Volume’ tab in the ‘Receptor Grid Generation’ window when preparing the Grid. You can include metal atoms as the place in the protein structure that you want ligands not to occupy.