[gmx-users] how to superimpose two structures of protein-ligand complex

[atsutoshi.okabe at takeda.com]

Dear all,

I would like to superimpose protein-ligand complex(including waters) after MD simulation to initial structure of the complex(including water) with protein backbone. 
I used g_confrms command like this.
$g_confrms -f1 initial.pdb -f2 after_MD.pdb 
And I select "Backbone" for Group of first and second structure file.
Then the only protein structure could be superimposed to initial structure, but the ligand structure could not.
Could you tell me how to superimpose both protein and ligand structure to initial structure? 

Bests,
Atsutotshi Okabe