I don t knwo whether it is possible to parametrize ligand and
optimize its position using simulated annealing and loop rmodeling,
so kind of imitating induced fit. Has anyone tried this and question
to Modeller Caretaker - is it potentially possible?
You can certainly treat ligands flexibly if you want, but you will need
to obtain topology and force field information for them:
Loop modeling uses a statistical potential that is derived from a
database of known (PDB) protein structures. It does not contain
protein-ligand interactions. So you will also have to add your own
interaction terms to simulate the binding between the ligand and the loop.