Force field parameter modification files were used to parameterize the flexible and constrained phosphotyrosines (see pty.frcmod and cpy.frcmod, respectively). The RESP partial charges for these residues were generated using the R.E.D. Server , and are included in the files PTY.mol2 and CPY.mol2. The RESP partial charges for the different ionization states of HEPES, also generated from the R.E.D. Server, are included in the files hepesa.mol2, hepesb.mol2, hepesc.mol2.