Point Mutaion on 4-chain protein

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

Dear Haddoc Users, Hi,

I am new here. I want to make point mutation on my 4-chain protein. I have already run the “ pdb_mutate.py ” script for each chain separately and obtained the four pdb files.

How can I proceed from here? Specifically, how can my system recover the missing atoms?

If I use the link below (and enter the # of molecules 4), the program asks me about the active residues.


If you could help me, I would appreciate.
Best regards,

Do you just want to use haddock to generate the mutations?

Then simply use the refinement interface of the server:


Submit your mutated model and haddock will generate all missing atoms and refine the model

Dear Prof. Bonvin,
Thanks for your quick reply.
Yes, I just want to use haddock to generate the point mutation at each chain.
I uploaded the mutated model to the link you sent, then I chose the “Water Refinement” protocol.
Haddock generated 4 models; however, the z score of the cluster-1 is zero. Would this be a problem?
Best regards,

By definition the z-score will be zero if you have only one point (cluster)

Thank you.