One-click-to-config-a-protein-ligand-MD-system (OCPLS)

Before using this script, please ensure that GROMACS and ACPYPE are installed. Name the protein structure file as protein.pdb and the small molecule file as mol.mol2. This script will automatically use three MDP files included in the archive (modifiable as needed) to set up the system. It employs the AMBER99-ILDN force field for the protein, the TIP3P water model, and GAFF2 for small molecule parameterization. The system will be prepared with energy minimization and equilibration steps, and a md.tpr file will be generated for a 100 ns molecular dynamics simulation.