Yes, you can.

"What fatal problems are expected to result from this?" None, if you are carefull, otherwise, it is really very difficult to guess.

Hello Hyun,

I would expect unexpected results/erroneous results. Both force fields have different parameterization methodologies; therefore, the parameters must be included consistently for each force field. For example, the charmm force field charges have been derived by QM calculations of explicit interaction energies with TIP3 water molecules, while amber derives the charges differently: by fitting to the electrostatic potential. Without validating the mixing of the two parameters, the results are unreliable.

Good luck!

Can you clarify which parts of the ligand cannot be parameterized? There might be a workaround. For instance, if is a metal complex you can just parameterize the organic backbone and manually add the missing metal to the topology.