HADDOCK error: TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!

Question

[sumayya_tariq]

Hi Everyone,

I have recently started working with HADDOCK stand alone and am facing some trouble running it. I wonder if anyone of you could help me in this regard.

I started with separating the 2 proteins in PDB ID: 2KTB, and then docking them with HADDOCK 2.1. But it is giving me the following error,

TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!
CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS
STRUCTURE NUMBER 1

I have set up the Upper distance limit for AIRs as 2.0 when generating the air.tbl file and all the other restraints as default in the run.cns file.

Any help would be highly appreciated.

Thanking You in anticipation.

[João Rodrigues]

Hi,

That means that your restraints are not properly defined. Which restraints exactly did you define?

[sumayya_tariq]

Thank You Mr. Rodrigues,

Like I said, I have kept all the restraints as default to start with and these have proved to work well with other proteins that were not part of the same PDB complex, unlike here in my case in which I am trying to validate HADDOCK by reproducing a PDB complex 1L4Z, I have also tried the same with 2KTB and it is giving the same error.

In the table below you can see the distance restraints (default) that I have defined.

Turn on/off and energy constants for distance restraints
                firstIteration     lastIteration     hot     cool1     cool2     cool3
distances       0                  2                 10      10        50        50
AIR (ambig)     0                  2                 10      10        50        50
hbonds          1                  2                 10      10        50        50

Do you want to randomly exclude a fraction of the ambiguous restraints (AIRs)?               *true       false

Number of partitions for random exclusion (%excluded=100/number of partitions)?              2

Do you want to use hydrogen bond restraints?                                                 true       *false

Do you want to define randomly ambiguous interaction restraints from accessible residues?
Only residues in the defined flexible segments will be considered Note that this option      true       *false
is exclusive with any other distance restraints and only for it0

Do you want to define center of mass restraints to enforce contact between the molecules?    true       *false
Note that these are only active during it0 and it1

Force constant for center of mass restraints                                                 1.0

Do you want to define surface contact restraints to enforce contact between the molecules?   true       *false
Note that these are only active during it0 and it1                                           

Force constant for surface contact restraints                                                1.0

[João Rodrigues]

Tip: Reply to my comment instead of providing an answer to your own question.

HADDOCK requires restraints to bring the molecules together. If you don't provide ANY distance restraints, it cannot work..

If you are trying to reproduce crystal structures, you can use Pymol to get a list of residues that comprise the interface of each molecule (e.g. A: 1,2,3,4,5,6,7 and B: 3,5,6,7). You can then input these as active residues.

If you don't have ANY information, you should enable the "center of mass restraints" option, but be aware that this has zero information on the interfaces (just pulls the proteins together) and the success rate will be much much lower. You should also increase the number of generated structures in each step to 10.000 (rigid body) - 400 (semi-flexible) - 400 (explicit solvent) in this case to have better sampling.