Unphosphorylated, protonated phosphorylated (charge: -1e), and deprotonated phosporylated (charge: -2e) serine, threonine, and tyrosine dipeptides were built in extended conformations using the tleap program of AmberTools 18 and either the AMBER ff99SB or FB18 force fields. As outlined in the leap setup script leaprc.phosaa10 (contained in Amber-Tools 18), the partial atomic charges for the phosphorylated amino acids were obtained from Homeyer et al., and modified Lennard-Jones radii for the phosphate oxygens were obtained from Steinbrecher et al. Each peptide was solvated in a truncated octahedron of 1380 to 1400 TIP3P 78 (for ff99SB) or TIP3P-FB 12 (for FB18) water molecules and neutralized by the addition of 1-2 sodium ions where applicable. The Joung-Cheatham monovalent ion parameters for TIP3P were used with the ff99SB/TIP3P simulations, while the same authors' monovalent ion parameters for SPC/E were used with the FB18/TIP3P-FB simulations, as the TIP3P-FB water model is closer in parameter space to SPC/E 80 than TIP3P.