Unable to Use Haddock 2.4 Submission

HADDOCK
1

I am trying to model a trimer protein complex which involves two identical chains and one different chain using the Haddock submission online page: HADDOCK - Input form.

However, after I submit the active residues in the Input Parameters tab and press next, the website will not move to the Docking Parameters tab. It simply reloads the Input Parameters page with all the same information still filled in. If I try to manually click the Docking Parameters tab, it gives a warning “No data have been found from previous step(s), please fill in “Input data” and “Input parameters” steps to be able to submit your HADDOCK run”. I am not sure why it will not save the information from the Input Parameters tab.

Here are is a screenshot of the input parameters page for the first molecule:

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Any help would be very much appreciated! I am not sure if I need to fill something out in the Input Parameters tab and that is why I am having this issue. I only entered the active residues and edited the binding partners in this tab. Please let me know

2

Always check the top of the page for possible error messages.

Trying clearing the cache and/or using a different web browser.

3

I have checked on a different browser as well and no error message appears and it will not move to the next tab.

4

Still something wrong on your side most likely.
The server is processing about 300 docking runs per day.

Describe exactly all what you are doing / inputting / changing on the server

And possibly share your input PDB files.

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5

I’ve looked over the server logs and could not find anything specific, and whatever you are finding should indeed raise an error.

Could you please tell us how you are defining restraints; how is each partner selection defined, did you add multiple groups (via the Add an active/passive selection set option)? A step-by-step description would be very helpful.

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6

Number of molecules - 3

The input PDB file is 2XQW for all and all marked as protein or protein-ligand:

Molecule 1 - Chain A
Molecule 2 - Chain B
Molecule 3 - Chain C

I have put one screenshot below and then the others in additional replies since I am not allowed to put multiple screenshots in one post

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Please let me know if there are any other details that would be helpful.

The binding partners are A+C (1+3), B+C (2+3), and C+A (3+1) & C+B (3+2).

10

Thanks for the detailed explanation! :slight_smile:

Which molecule do these refer to? In you screenshots it says Selection #3 two times.

Did you get to this step by clicking Add an active/passive selection set (max. 2) on molecule 3?

Also, what is the operating system and browser in which you encountered this issue?

11

Yes, I clicked Add an active/passive selection set (max. 2) on molecule 3. Molecule 3 binds to both molecules 1 and 2, explaining the need for two selections.

I am using Windows 10 and have experienced the issue in Google Chrome and Mozilla Firefox.

12

I cannot replicate the error, I’ve tested setting up the scenario you described in the screenshots and the submission goes trough:

Mol1 Sel1 - Mol3
—
Mol2 Sel1 - Mol3
—
Mol3 Sel1 - Mol1
Mol3 Sel1 - Mol2

https://bianca.science.uu.nl/haddock2.4/run/1524990235/127049-3-body-test

So it could be something related to the browser, please try cleaning the browser cache and maybe even updating it.

Alternatively if that still does not work, you might be able to get away with editing the parameter file (the job_params.json file) manually, adding your active/passive residues and submitting it via the file submission interface.

13

Okay, thank you for providing the results of the job! Not sure why I am having so much trouble with it.

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