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

ms devicerandom at gmail.com
Mon May 19 13:16:33 CEST 2014

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.


> 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

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