Docked proteins are separated


I submitted a dimer as the receptor and a single chain protein as the ligand using the easy interface. Docking was finished successfully and scores and interaction energies seem normal. However, when I visualize the clusters in VMD, proteins are separated in space. I tried searching the manual and tools but couldn’t find any similar issues. Could you kindly help me fix it?

I really appreciate your help.

Best Regards

1 Like

Is your dimer separated in space? Or the dimer with the other protein?

Did you renumber the dimer to avoid overlap in numbering?

Are you using a local version of HADDOCK or the web server?

Dimer with the other protein.

Yes, I did.

I used the web server.


Then most likely a problem with your restraints I would say. Can you share (via email) the link to your result page?

Sure, which email address? Thanks!