The present work demonstrates that the crude approach of simply deleting Hessian matrix elements can be an effective way to eliminate imaginary vibrational frequencies in the presence of fixed-atom constraints, yet this simple approach is not without limitations. It tends to underestimate the ZPE, which can hinder the prediction of reaction thermochemistry and kinetics, convergence with respect to model size is sometimes erratic, and finally the fixed-atom technique introduces artificial rigidity that is evident in steeper torsional potentials for conformational changes within the active site. In contrast, the use of harmonic confining potentials is equally simple yet preserves the number of vibrational modes, resulting in a more realistic representation of vibrational contributions to thermochemistry and barrier heights. Application of harmonic restraints to an enzyme-catalyzed decarboxylation reaction, using various active-site models containing 76-189 atoms and necessitating numerous anchor atoms, reveals that convergence with respect to model size is generally better than what is observed using fixed-atom restraints. The simplicity of the harmonic approach suggests that this should be the default paradigm for quantum-chemical cluster modeling of enzyme active sites.