Fatal error: Residue 'EDO' not found in residue topology database

You won’t find an exact solution for your exact residue. But the answer is always the same in every post you will find - pdb2gmx can only handle species that already exist in force field .rtp files. It’s not magic. If you have a nonstandard species, you have to parametrize it yourself or use external (non-GROMACS) programs to write a topology.