# Can I leave the active residue list option blank? **URL:** \ **Category:** HADDOCK\ **Created:** [March 9, 2019, 8:20am UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477 "2019-03-09T08:20:53Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Sushmita\_Basu](https://avatars.discourse-cdn.com/v4/letter/s/47e85d/32.png) [@Sushmita\_Basu](https://ask.bioexcel.eu/u/Sushmita_Basu)\ **Post date:** [March 9, 2019, 8:20am UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/1 "2019-03-09T08:20:53Z")
Hi, I have a protein of 99 residues and RNA of 12 nucleotides. The chemical shift perturbation info for the protein is available based on which i selected the active residues of the protein. But for the RNA i have no info regarding the binding nucleotides. How shall I guide the docking for a reliable pose? Thanks ---
**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:** [March 9, 2019, 10:07am UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/2 "2019-03-09T10:07:10Z")
You might define the entire RNA as passive in HADDOCK. But no warranty you will get “reliable” poses… ---
**Author:** ![Sushmita\_Basu](https://avatars.discourse-cdn.com/v4/letter/s/47e85d/32.png) [@Sushmita\_Basu](https://ask.bioexcel.eu/u/Sushmita_Basu)\ **Post date:** [March 9, 2019, 1:00pm UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/3 "2019-03-09T13:00:20Z")
Thanks for the prompt response. Another doubt i have is that, there is a 4 nucleotide motif in this 12 nt long RNA which is, according to some selex experiment, important for the binding. Now since am not sure if all of those 4 nucleotides do make any contact with the protein or not,if at all any, will the docking be biased if i provide those residues as active site? ---
**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:** [March 9, 2019, 3:44pm UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/4 "2019-03-09T15:44:17Z")
By default on the easy interface 50% of the restraints are randomly discarded for each docking run. You can also perform a run without those as active and one with. And compare the results. ---
**Author:** ![Sushmita\_Basu](https://avatars.discourse-cdn.com/v4/letter/s/47e85d/32.png) [@Sushmita\_Basu](https://ask.bioexcel.eu/u/Sushmita_Basu)\ **Post date:** [March 9, 2019, 4:29pm UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/5 "2019-03-09T16:29:32Z")
Thanks. Infact I already tried doing the docking by keeping the active residue section blank, but it gave error: “(”\:", ConstructionError(’\nAn error has occurred in the construction of a HaddockRunData object\nNumber of arguments: value 0, keyword 7\n\n\*\*\* (HaddockRunData) Value/Keyword constructor \*\*\*\nMember i:\n **Protein 2 has no active residues defined. Therefore, it is meaningless to define passive residues on protein 1.** Please remove the passive residues on protein 1.\n\nProtein 2 has no active residues defined. Therefore, it is meaningless to define passive residues on protein 1. Please remove the passive residues on protein 1.’,)) Am i going wrong somewhere? ---
**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:** [March 9, 2019, 4:43pm UTC](https://ask.bioexcel.eu/t/can-i-leave-the-active-residue-list-option-blank/1477/6 "2019-03-09T16:43:07Z")
The answer is in the last sentence of the error message you got… _Please remove the passive residues on protein 1_