genbox -cs spc216.gro -box 5 5 5 -o water_box.gro

grompp -f em.mdp -c water_box.gro -p system.top -o water_wo_ions.tpr

genion -s water_wo_ions.tpr -pname Fe -pq 3 -o system_b4em.pdb -neutral -conc 0.15 -p system.top

//done up to here

grompp -f em.mdp -c system_b4em.pdb -p system.top -o system_em.tpr //errors "No such moleculetype Fe"

mdrun -v -deffnm em