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

Lenin Kandasamy leninkandasamy at gmail.com
Mon May 19 13:15:25 CEST 2014

Hi Atsutotshi,

Yes, g_confrms module computes RMSD the after least squares fitting of the
latter on the first structure. If you interested in comparing the
interactions between two protein-ligand complexes, I suggest you try
PDBeFold. Please check this link,
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver. You can also try WHATIF
for comparing the interactions.
I hope this helps.

Thanking you,
Lenin Kandasamy
Graduate Student (Final Semester),
Centre for Biotechnology,
Anna University, Chennai- 25
+919176149739 / +918095793759

On 19 May 2014 16:11, <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.
> 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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