A principal component analysis is applied to the study of dipeptides corresponding to the 20 naturally-occurring amino acids and Avian polypeptide, APP, to quantitatively assess (1) force field parametric and (2) structural relations. The parametric principal component analysis has provided insight into the relationship between the molecular structure and the potential energy function. The molecular structures are most sensitive to the bond and angle reference parameters. The nonbond parameters also significantly influence molecular structure. The structural space of the dipeptides and APP is very closely linked to the parameter space of the potential. The bond length and bond angle internals are tightly controlled by the bond and angle reference value parameters. Torsional motion is the most sensitive degree of structural freedom and is generally controlled by nonbonded influences. In the second part of the research, principal component analysis of the molecular structure Green’s function matrix provides a means to elucidate how the molecular structure will respond to internal forces introduced in the molecule. The eigenvectors of the Green’s function matrix corresponding to the maximum eigenvalues determine the internal coordinates responsible for the largest molecular responses. It is found that the torsional degrees of freedom are responsible for the greatest molecular response. To complement the analysis of APP, the sensitivities of centroids associated with each residue to changes in the backbone internals were determined. The coefficients indicate the local molecular response and were found to be in agreement with previous characterization of regional flexibility.