Can I leave the active residue list option blank?

HADDOCK
1

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

2

You might define the entire RNA as passive in HADDOCK.

But no warranty you will get “reliable” poses…

3

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?

4

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.

5

Thanks. Infact I already tried doing the docking by keeping the active residue section blank, but it gave error:

“(”<class ‘spyder.ConstructionError’>:", 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?

6

The answer is in the last sentence of the error message you got…

Please remove the passive residues on protein 1