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!

6

Hi，I’m undefined any active/passive in step2, but I can’t skip step2 and fill in ambig file. Could you please help me solve this question? thank you!

7

Hi zhangjian,

To be able to input an ambiguous restraint file in the webserver, you need to be in expert/guru mode (not available in easy mode).

You can request your account to be elevated to expert mode in the webserver.
On the user dashboard, click on request elevated permission button and fill the form.
This requires a manual validation but you can expect it to be done within a day.

8

Do you have higher level access? If not request it in your registration page.

9

oh, very grateful