Point Mutaion on 4-chain protein

HADDOCK
1

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.

https://wenmr.science.uu.nl/haddock2.4/submit/1

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

2

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

Then simply use the refinement interface of the server:

https://wenmr.science.uu.nl/haddock2.4/refinement/1

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

3

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,

4

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

5

Thank you.
Sincerely,
Deniz