Simulating a protein with two chains and two identical ligands

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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,


You probably copied the same ligand twice.