Docking 3 molecules using webserver

HADDOCK
1

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.

2

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

3

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

4

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.

5

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:

6

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