The final step in parameterizing the trypsin-benzamidine complex involves solvating the system with water molecules and applying periodic boundary conditions. This ensures that the simulation accurately represents the behavior of the complex in an aqueous environment while accounting for long-range interactions and avoiding edge effects. Additionally, counterions are added to neutralize any net charge in the system, creating an electrically neutral simulation system. We execute the following command in the terminal to parameterize the trypsin-benzamidine complex: