Protein modified after completing the docking process

[AlvaroBQ]

Well, i run a protein-protein docking some days ago.

Structures used:

• Trimmer structure (375 amino acid long )
• Monomer structure (86 amino acid long)

The problem begin when i decide to analyze the results of the docking. In all the cluster generated the first structure (trimmeric one) was modified and doesnt have any concordance with the original structure or any structure of a protein cause the tertiary structure looks broken, with lot of amino acid unlinked.

I used the easy interface for docking, and set all the residues of both proteins like “active residues”.

This its the link of my job : http://milou.science.uu.nl/serviceresults/HADDOCK2.2/7904636898/TRIMEROPRUEBA2/

I would very thankfull if someone could help me with this error, cause I cant elucidate it.

[amjjbonvin]

Did you renumber your trimer to avoid overlap in numbering?
Check the forum for tips on how to handle homomers, e.g.:

Setup for protein dock to protein homodimer

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2 Hello, Does anybody know how to setup protein to dock a protein homodimer. Since there are two chains in a homodimer (A subunit and B subunit), how can I assign the residues in A subunit and/or in B subunit. What is the format I should use. Please let me know. Thank you, Han

Error submitting a trimmer structure for docking

Im doing protein-protein docking and after submitting my trimmer on the haddock server, i get this message saying: There was an inconsistency in your data Error message First pdb file contains multiple chains with overlapping numbering: P1 - B1 What can i do if i already rename every segment and chain of my trimmer to prevent the “overlapping”, or in which part im failing? By the way, its a homo-trimmer protein. Thanks, by the way.

But looking at your exploded models, I suspect your starting models are not of very good quality and must have clashes…

[AlvaroBQ]

Yes, indeed, i renumbered my trimer to avoid overlaping. Thanks about the topics about my problem Dr Bonvin.