[modeller_usage] Close contacts between protein and ligand

Hi I'm modeling protein with ligands (using the "." options in the sequence file). However, in the final models the contacts between protein side chains and ligands are too close (the template and target have differently sized ligands; the template target ligand has a smaller ligand). Is there a way to avoid this, like giving less weight to the homology terms and greater weight to the standard FF terms? Thanks, Dan