This command solvates the receptor-ligand complex, represented by the variable receptor_ligand_complex, in a truncated octahedral box using TIP4Pew water molecules. The truncated octahedral shape is preferred over a simple cubic box due to its more efficient use of space, reducing the number of water molecules required to solvate the system. The specified padding of 8 Å creates a buffer region around the protein to prevent any artifacts from periodic boundary conditions. • addIons2 mol Cl-7: Since the system has a net positive charge, adding chloride ions (Cl-) neutralizes the overall charge. When setting up simulations, it is generally recommended to carefully consider the ions present in the experimental or physiological conditions to mimic the real environment closely. However, in this specific scenario, the decision to use only chloride ions is based on the information available and the challenges associated with including other ions.