Three protein complex docking: Pairing error

HADDOCK
1

I am currently conducting the docking of three proteins. The input parameters for the interaction interface is as follows.

  • Molecule 1：
    Selection 1 —Pair to active/passive selection set number：4
    Selection 2 —Pair to active/passive selection set numbers：3,5

  • Molecule 2：
    Selection 3 —Pair to active/passive selection set number：5
    Selection 4 —Pair to active/passive selection set number：1

  • Molecule 3：
    Selection 5 —Pair to active/passive selection set number：3

However, why does the system return an error message as follow for the Selection 5 of Molecule 3:

Selection cannot contain itself.

I’d be grateful for a fix or a way to bypass this issue.

2

in the mean time you could try to generate a restraint file with the gentbl server and upload it as ambig file in the haddock server.

Check: https://rascar.science.uu.nl/gentbl/

And make sure you did not assign similar chainIDs to your various molecules

3

Thank you very much for your assistance!

I have successfully generated a restraint file using the gentbl server, but encountered an issue when attempting to upload it to the HADDOCK server. Specifically, I am unable to proceed past the problematic Step 2 (Input parameters) to reach Step 3 (Docking parameters) where the generated ambig file should be uploaded. Could you please advise on how to properly utilize my ambig file under these circumstances?

4

don’t define any active / passive in step 2

5

Thank you so much for your help! The submission finally succeeded!