Figure 8.

(A) (A) Four ligands for testing ALB and RLB modules. For the relative binding FEP/MD, the gray arrows and the red colors (atoms and bonds) are used for the perturbation paths and the single topology (unperturbed) region, respectively. (B) Overlaid stick representations of four ligand initial structures (benzene in orange, toluene in yellow, ethylbenzene in green, and propylbenzene in blue) in T4 lysozyme (gray). The aromatic ring of four ligands was well aligned based on the reference ligand (toluene). (C) A representative snapshot of T4-lysozyme-toluene complex in a solution box: gray cartoon for T4-lysozyme, yellow sphere for toluene, magenta and green beads for K⁺ and Cl⁻ ions, respectively.