# Three protein complex docking: Pairing error **URL:** \ **Category:** HADDOCK\ **Created:** [June 8, 2025, 8:59am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740 "2025-06-08T08:59:37Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Charlene](https://avatars.discourse-cdn.com/v4/letter/c/eada6e/32.png) [@Charlene](https://ask.bioexcel.eu/u/Charlene)\ **Post date:** [June 8, 2025, 8:59am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/1 "2025-06-08T08:59:37Z")
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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [June 8, 2025, 9:21am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/2 "2025-06-08T09:21:32Z")
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/](https://rascar.science.uu.nl/gentbl/) And make sure you did not assign similar chainIDs to your various molecules ---
**Author:** ![Charlene](https://avatars.discourse-cdn.com/v4/letter/c/eada6e/32.png) [@Charlene](https://ask.bioexcel.eu/u/Charlene)\ **Post date:** [June 8, 2025, 12:27pm UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/3 "2025-06-08T12:27:41Z")
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? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [June 8, 2025, 2:34pm UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/4 "2025-06-08T14:34:08Z")
don’t define any active / passive in step 2 ---
**Author:** ![Charlene](https://avatars.discourse-cdn.com/v4/letter/c/eada6e/32.png) [@Charlene](https://ask.bioexcel.eu/u/Charlene)\ **Post date:** [June 9, 2025, 12:42am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/5 "2025-06-09T00:42:19Z")
Thank you so much for your help! The submission finally succeeded! ---
**Author:** ![zhangjian](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/zhangjian/32/1219_2.png) [@zhangjian](https://ask.bioexcel.eu/u/zhangjian)\ **Post date:** [July 15, 2025, 6:36am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/6 "2025-07-15T06:36:24Z")
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! ---
**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Post date:** [July 15, 2025, 6:54am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/7 "2025-07-15T06:54:20Z")
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. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 15, 2025, 6:55am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/8 "2025-07-15T06:55:29Z")
Do you have higher level access? If not request it in your registration page. ---
**Author:** ![zhangjian](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/zhangjian/32/1219_2.png) [@zhangjian](https://ask.bioexcel.eu/u/zhangjian)\ **Post date:** [July 15, 2025, 6:56am UTC](https://ask.bioexcel.eu/t/three-protein-complex-docking-pairing-error/5740/9 "2025-07-15T06:56:57Z")
oh, very grateful