Enlighten2 is specifically designed for basic and efficient protein-ligand simulations and therefore currently has some limitations. At least one non-covalently bound ligand is required. Automatic parameterization of (additional) covalently bound ligands, cofactors or custom residues is not supported, but the corresponding parameters can be provided manually. (Currently, covalent bonds between protein and non-protein, e.g. cofactor, residues cannot be added through the plugin.) The solvation and MD simulation are limited to a sphere, with all atoms outside the sphere fixed (to avoid the computational cost of simulating fully solvated systems with periodic boundary conditions). This means that large conformational changes or full ligand dissociation cannot be studied. Finally, since Enlighten2 ligand parameterization relies on Antechamber, Enlighten2 only supports the ligand chemistries covered by the General Amber Force Field, GAFF.