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

[ms]

On 5/19/14 12:41 PM, atsutoshi.okabe at takeda.com wrote:
> 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.
If you only want to visualize/save a PDB of the superimposition, I would 
use the protein visualization program UCSF Chimera and the structure 
alignment tools provided in it. It will keep the ligands and everything 
for both files you upload.

cheers,
m.

> 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
>