Triple protein complex docking - selection numbering issue during restraint setup


I’m trying to obtain a model of a tripartite protein complex. Two proteins are already in complex, but I split them into separate pdbs. All three were loaded successfully, then I proceeded to setting up restraints. I’ve been trying to define 2 active residue selections for each protein (6 total):

  • resid in Mol1 towards Mol2
  • resid in Mol1 towards Mol3
  • resid in Mol2 towards Mol1 etc.(defined by ‘partner selection’)
    Each selection can be shown on protein structure, but I cannot proceed to the docking parameter setup. There’s no error box present despite multiple attempts. I’ve tested both Firefox and Chrome on Ubuntu 20 workstation, clearing the browser cache did not solve the issue.

Though I’ve just noticed that upon start of input parameter setup, the selection numbers (#) are duplicated inside each molecule: Mol1 has 2x Sel1, Mol2 has 2x Sel2, Mol3 has 2xSel3.

I’ve tried removing additional selections and adding them again to fix the numbering, ending up with selections 1&2 for Mol1, 2&4 for Mol2 and 3&6 for Mol3. It appears that selection numbering for Mol2 is dependent on Mol1, numbering for Mol3 is dependent on Mol1 & Mol2, but I see no way to change the Mol1 numbering.

This causes numbering overlap between the second selection of Mol1 and first selection of Mol2.
Despite multiple attempts, I haven’t been able to fix the issue and proceed further with my docking jobs.
I’d be grateful for a fix or a way to bypass this issue.

Best regards,

Below you can see the effect of removing restraints and adding them again

Same as above, but without second Mol2 selection

and finally behavior of Mol1 second selection alone