I try to run 'FEP Protein Mutation for Ligand Selectiviry' function from Schrödinger Maestro. I uploaded different protein/ligand complexes from PDB and performed 'Protein Preparation Workflow', but with all complexes were the same problem: program doesn't recognize the ligands: "Number of ligands: 0".

It shows my ligand as a residue in protein sequences.

While other functions in Maestro recognize it as ligand. Including 'Protein Preparation Workflow': it also recognized it as ligand.

In 'Ligand Detection' section of 'Preferences' I indicated those molecules as Ligands.