Centering ligands and protein

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I have a simulated a system of protein with two ligands. to centre the protein I ligand, I made index file consisting of protein and ligand. then i centred using following commands-


gmx trjconv -s step4.0_minimization.tpr -f output.xtc -o outputwhole.xtc -pbc whole -dt 10 n ligand.ndx
gmx trjconv -s step4.0_minimization.tpr -f outputwhole.xtc -o outputcluster.xtc -pbc cluster -dt 10 -n ligand.ndx
gmx trjconv -s step4.0_minimization.tpr -f outputcluster.xtc -o outputbox.xtc -pbc mol -center -dt 10 n ligand.ndx


however in the pdb from trajectory, ligands are not centred. how can i centre the ligand?

Another question, can we output more than groups (eg protein and ligand) instead of using index file becuase gromacs have grouped them already.
Appreciate your reply.

Thank you
Best Regards

did you try in the last step to use only -center?
sorry I do not understand the last question. Can you reformulate?