MD simulation has been widely used for investigating the interaction properties between molecules in a system. In this study, all MD simulations were performed using GROMACS software (version 4.5.5) (26). The ALX/FPR2 protein structure was processed by using tip3p water mode and AMBER99SB force field to generate coordinates and topology files (27). Then, the ligands were dealt with antechamber and tleap tools from AmberTools9 (28), and the ligand’s topology was created by using the ACPYPE tool (29). The simulations were carried out under periodic boundary conditions, with a cubic periodic box setting the minimal distance of 1.0 Å between the protein and edge of the box. To neutralize the system, ions (Na+ and Cl) were added with a salt concentration of 0.15 M. Then, the system was energy-minimized using steepest descent minimization algorithm until the maximum force under 1000 kcal mol−1 nm−1. Then, we equilibrated the protein-ligand complex with 100-ps NVT equilibration (constant number of particles, volume, and temperature) to stabilize the system at 300 K and NPT (constant number of particles, pressure, and temperature) equilibration within 100 ps. After the equilibration steps, the system was well optimized, and a period of 20-ns MD simulations with a time step of 2 fs at constant pressure (1 atm) and temperature (300 K) was conducted. During the simulation process, energy and trajectory information were collected every 2 ps, long-range electrostatics was investigated by the particle mesh Ewald method (30), and all bond lengths were limited by LINCS algorithm (31).

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