I am working with a protein with a bound small molecule (non-covalent). I've managed in creating parameters for the ligand and relaxing the complex following this workflow: https://new.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README
Next I'd like to do the same but including some ligand flexibility. I've generated conformers and new parameters, but when I try to relax the complex, the ligand coordinates are wrong. Not sure if there is something that I should do differently.
For context, I'm allowing a limited set of conformational flexibility to my ligand - just sample one small substituent exposed to solvent and generate aprox. 5 conformers. I would like my ligand core to stay in place and sample different conformations for the substituent. Is this possible? Is there an example of a workflow like this?