The initial structures for simulated systems were taken from crystal structures of wild-type human CypA bound to HIV capsid protein, PDB entries 1M9C and 1M9Y. In both cases, chain A was taken as the structure of the CypA receptor, and the substrate was trimmed to a six-residue model peptide, of sequence HAGPIA from PDB 1M9C (with the G-P peptide bond in the trans configuration), or AAAPIA from PDB 1M9Y (with the A-P peptide bond in the cis configuration). Substrate N and C termini were not capped and peptides were modeled in their zwitterionic states. Basic and acidic residues were modeled in their ionized states and histidine residues modeled in their neutral, Nd-protonated form. Finally, R55A mutant structures with equivalent cis-and trans-proline substrates were created by manually truncating the Arg55 residue in the crystal structures to the Cb atom.