Simulating a protein with two chains and two identical ligands

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hi all,

I’m simulating a protein with two chains (A + B). Each chain has a ligand bound to it. Both ligands are identical. I was following the protein-ligand tutorial on gromacs. When I visualise my processed complex file (complex.gro), I can see both ligand are overlapping rather than bound to their respective chains. Is there a way I can correct this? Any help would be appreciated.

Many thanks,

Akash

You probably copied the same ligand twice.