Docking 3 molecules using webserver

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

I am trying to dock 3 molecules: one protein and 2 peptides. I can’t get past the input parameters page, no errors are flagged but something is clearly not satisfied. I have done the ‘partners selection’ (molecule 1 interacts with both 2 and 3, molecules 2 and 3 only interact with molecule1 not each other).

I think the problem might be to do with the active and passive residue selection. However, I have docked both peptides with the protein separately and these were successful. They will both compete for the same site and I was hoping by docking both proteins simultaneously this might help identify an allosteric site.

Any help getting past the input parameters page would be great.

Any error message appearing on top of the window when you try to click on next?
These are usually appearing in a red box.

No errors appear, when pressing next it just goes back to the top of the page.

Are there any tutorials that can provide guidance for filling in this page?

Thank you

We have several tutorials online at Education & Tutorials of the Bonvin Lab – Bonvin Lab

Did you try to start from scratch after cleaning your cache?

Also if you want support, describe exactly what you are doing/filling in that problematic page.

Thank you, I have had another go this morning and was successful. The input parameter page generated an extra ‘active and passive residues’ tab for each molecule. I had previously been trying to fill them all in as I assumed they were all needed. Instead I removed the extra tabs so each molecule only had one ‘active and passive residue tab’ and it ran successfully. :slight_smile:

Glad to hear that - there are so many options that it can become confusing.