To further analyze ligand interactions for some of the above models, the structures were divided into ligand and protein pdb files. The separate structures were protonated: the protein with VMD (Visual Molecular Dynamics, v1.9.4) and the ligand with Avogadro v1.2.0. VMD was used to generate a psf (NAMD protein structure file) file for the protein and the Ligand Reader and Modeler from charmm-gui.org, was used to generate the psf and prm files for the ligand. VMD was then used with the CHARMM36 forcefield to re-combine the ligand and protein, thus solvating the structure and generating the required psf and pdb files . NAMD v2.14 was used to run 100 steps of minimization followed by 100 ns of dynamics with 2fs/step (50,000,000 iterations). The simulation conditions were rigid bonds involving hydrogen (rigidbonds set to "all"), a splitting distance of 12A between the short range and PME long range potential, Langevin dynamics at 310K with hydrogen atoms excluded (Langevin hydrogen set to "off"), and Periodic Boundary Conditions .