For each protein-ligand system, a protein in complex with a ligand was solvated in a periodic dodecahedral water box (TIP3P model 36 ) containing 0.1 M NaCl solution with a margin of 12 Å from the protein. Lysine, Arginine, Asparagine, Glutamate, and the N and C termini were in their charged states, and the protonation state of histidine was determined using the GROMACS command, pdb2gmx. The ligand topologies in the Amber format were converted to the GROMACS format by acpype python script . After energy minimization, each system was equilibrated in the constant volume and constant temperature (NVT) ensemble at 300 K for 100 ps and in the NPT ensemble at 1 atm for 100 ps with harmonic position restraints on the mainchain atoms. The time step was 2.0 fs. Bonds involving hydrogen atoms were constrained using a LINCS . Non-bonded interactions were cut off at 10.0 Å. The electrostatic interactions were computed using the particle-mesh Ewald method .