The apo structure of T4L99A was protonated according to a pH of 7.0 using PDBFixer. Missing loops were added where appropriate and protein termini were capped using N-methyl and acetyl caps. Each system was then solvated in a box of TIP3P water with a buffer of 12 Å around the protein. NaCl ions were added to neutralize the system and up to a salt concentration of 0.15 M.