I am currently working on metal–natural compound complexes. My workflow involves:

While I am able to visualize the ligand interactions in Discovery Studio, I am facing two main issues:

• The software gives an error: "Ligand is not a single fragment"
• As a result, I am unable to generate the secondary structure of the protein and unable to display the 2D structure diagram of the docked ligand complex.

My Questions:

Any advice or experiences with similar metal–ligand docking workflows would be extremely helpful.

Thank you!