Hi,

I conducted virtual screening for a database using AutoDock Vina and encountered an issue with molecules containing non-bonded ions (e.g., cations like K+ or anions like Cl-, F-).

It appears that AutoDock Vina treats these ions as separate fragments, which prevents the docking process from running properly.

Could you please assist me in understanding how to handle such ligands for docking?

For your reference, I have attached a screenshot of one such ligand.

Thank you.