Can we use AmberS99 for antibody (protein) and Charmm36 for antigen (drug like small non-protein) in md simulations? Or do we have to use only one forcefield for both?
If you want to study their complex, you have to use the same force field for both components. Think about how would it even be possible to model their contact surface if you use different force fileds for each one.
You might choose CHARMM36 for both, it supports CHARMM General Force Field (= CGenFF), which is designed to model small organic molecules.