Create a protein–ligand system
This stage parameterises the selected ligand with ACPYPE/Antechamber, prepares the repaired protein with pdb2gmx, combines both in the bound coordinate frame and validates the assembled topology with grompp.
Scientific safeguard: this version does not silently guess the ligand formal charge. SDF/MOL2 is preferred because PDB files do not store reliable bond-order information.