Simulations of both WT and R55A mutant CypA, bound to cis-and trans-proline substrates, were performed in triplicate using the AMOEBA polarizable force field. A control simulation of WT CypA bound to the cis-proline substrate was also performed with the Amber ff14SB additive force field. See Table for a list of all simulations performed. Initial protein crystal structures were protonated and solvated using the tleap module of the Amber14 package. CypA-peptide complexes were neutralized with Cl -anions, solvated in an approximately 63 x 65 x 62 Å periodic box of water such that no solute atom was less than 8.0 Å from the box edge, and Na + /Cl -ions added to create a 150 mM NaCl ionic atmosphere. The simulation of the WT CypA cis-proline system performed with the Amber additive force field used the same starting configuration as the first AMOEBA replicate, except ion positions in bulk solvent were randomized. In total, system sizes varied from 17727 atoms (R55A trans-proline system), to 19030 atoms (R55A cis-proline system).