Distorted output structures

[gabrielep]

Hello,

I’ve installed local version of haddock2.4 and I’m trying to dock large multi-chain complexes (>10 chains).

I followed the protein-protein docking tutorial and, on top of that, I only modified the run.cns file turning on the center of mass restraints and increasing the sampling as it is stated in this post:

Protein Protein docking without restraint definitions

Hi Prof. Bonvin, I have experienced with bound ligand protein-protein docking with restraint definition with 5A active site residue from the ligand. HADDOCK generated almost similar poses as reference. Now, assume if I don’t have information about ligand in the second protein. I don’t know the second protein where exactly bind with the first protein. Blindly, I would like to submit a job. Is it possible to submit a job without defining active and passive residues in HADDOCK interface? If yes th…

Runs seems to complete successfully but in the ave.pdb results I find completely distorted structures. I also tried using just 2 chains, and the amount of distortion seems lower but still the structures are completely destroyed.

Do you have any idea of why this is happening?

[amjjbonvin]

The average file has no meaning…especially not if many different models are generated. Look at the individual models.

[gabrielep]

Oh that was quite simple.
I got tricked checking an avg.pdb file from a sample run you provided somewhere, which actually contains a good structure.

Sorry for the silly question and thanks for your answer