Restraints violation

HADDOCK
1

Hi,
I want to dock a peptide and protein.
I have some ambiguous restraints that I see from the NOESY NMR spectrum.
But for some reason the HADDOCK results do not match the restraints and the restraints violation in the result page equals 0.
How can I fix this?
I didn’t add any unambiguous restraints and made sure it calculates all hydrogens.
Also, how many iterations is recommended?

my restraints are:
assign(segid A and resid 24 and name HD)(segid B and resid 3 and name HG*) 3.5 2.0 2.5
assign(segid A and resid 24 and name HD)(segid B and resid 3 and name HD1) 3.5 2.0 2.5
assign(segid A and resid 24 and name HD)(segid B and resid 3 and name HD2) 3.5 2.0 2.5
assign(segid A and resid 68 and name HD)(segid B and resid 3 and name HD1) 3.5 2.0 2.5
assign(segid A and resid 68 and name HD)(segid B and resid 3 and name HD2) 3.5 2.0 2.5
assign(segid A and resid 52 and name HH)(segid B and resid 5 and name HG*) 3.5 2.0 2.5
assign(segid A and resid 52 and name HH)(segid B and resid 5 and name HB) 3.5 2.0 2.5
assign(segid A and resid 24 and name HE)(segid B and resid 3 and name HD1) 3.5 2.0 2.5
assign(segid A and resid 24 and name HE)(segid B and resid 3 and name HD2) 3.5 2.0 2.5
assign(segid A and resid 52 and name HZ3)(segid B and resid 5 and name HG*) 3.5 2.0 2.5
assign(segid A and resid 52 and name HZ2)(segid B and resid 5 and name HG*) 3.5 2.0 2.5
assign(segid A and resid 52 and name HZ2)(segid B and resid 5 and name HB) 3.5 2.0 2.5
assign(segid A and resid 48 and name HD*)(segid B and resid 11 and name HZ2) 33.5 2.0 2.5
assign(segid A and resid 48 and name HD*)(segid B and resid 11 and name HZ3) 3.5 2.0 2.5
assign(segid A and resid 48 and name HD*)(segid B and resid 11 and name HH2) 3.5 2.0 2.5

Is this not enough?

Thx,
Miriam

2

Two things:

  1. Turn on the option to keep all hydrogens as by default all non-polar hydrogens are removed

  2. Make sure that the naming matches the naming in the PDB file

Or as solution to both points: define the restraints to the heavy atoms (with a small correction on the upper limit.

3

Thx!
how can I define the restraints to the heavy atoms with a small correction on the upper limit?

4

Simply change the atom name to the heavy atom to which the hydrogen it attached to.
And add 1A to the upper limit

5

Hi Thank you
I’ve tried this many times and it still does nit work and some of the restraints are not kept.
is there a problem with my format? maybe the * is confusing HADDOCK? spaces? or any other reason?
I cant think of anything else.
Here are the list when the are between carbon atoms:
assign(segid A and resid 24 and name CD*)(segid B and resid 3 and name CG*) 4.5 2.0 2.5
assign(segid A and resid 24 and name CD*)(segid B and resid 3 and name CD1) 4.5 2.0 2.5
assign(segid A and resid 24 and name CD*)(segid B and resid 3 and name CD2) 4.5 2.0 2.5
assign(segid A and resid 68 and name CD*)(segid B and resid 3 and name CD1) 4.5 2.0 2.5
assign(segid A and resid 68 and name CD*)(segid B and resid 3 and name CD2) 4.5 2.0 2.5
assign(segid A and resid 52 and name CH*)(segid B and resid 5 and name CG*) 4.5 2.0 2.5
assign(segid A and resid 52 and name CH*)(segid B and resid 5 and name CB) 4.5 2.0 2.5
assign(segid A and resid 24 and name CE*)(segid B and resid 3 and name CD1) 4.5 2.0 2.5
assign(segid A and resid 24 and name CE*)(segid B and resid 3 and name CD2) 4.5 2.0 2.5
assign(segid A and resid 52 and name CZ3)(segid B and resid 5 and name CG*) 4.5 2.0 2.5
assign(segid A and resid 52 and name CZ2)(segid B and resid 5 and name CG*) 4.5 2.0 2.5
assign(segid A and resid 52 and name CZ2)(segid B and resid 5 and name CB) 4.5 2.0 2.5
assign(segid A and resid 48 and name CD*)(segid B and resid 11 and name CZ2) 4.5 2.0 2.5
assign(segid A and resid 48 and name CD*)(segid B and resid 11 and name CZ3) 4.5 2.0 2.5
assign(segid A and resid 48 and name CD*)(segid B and resid 11 and name CH2) 4.5 2.0 2.5

6

Can you share the link to the run, so that we can check if all restraints are properly read in.

If this is the case it could be you have some inconsistent restraints or more conformational changes are required

7

yes, thank you!
I ran a lot of them (with both restraints on hydrogens and carbons), attached are two different structures I tried to dock (they have different restraints):
https://wenmr.science.uu.nl

https://wenmr.science.uu.nl

Thank you!

8

The links are to the home page of our server and not the specific runs…

9

Sorry about that
https://wenmr.science.uu.nl/haddock2.4/result/7747164191/234918-QKC_1H_2804

https://wenmr.science.uu.nl/haddock2.4/result/7747164191/234916-QKC_2H_gui

10

To check that your restraints are properly read, edit e.g. the complex_run1_it0_refine_1.out file which you can find after downloading and unpacking the full archive of the run.

Then search for: NOE>assign

and check that atoms are selected for all your restraints. A quick check of the QKC_1H_2804 runs gives the following problems:

assign(segid A and resid 24 and name HE*)(segid B and resid 11 and name HG*) 3.5 2.0 2.5
SELRPN: 2 atoms have been selected out of 1100
SELRPN: 0 atoms have been selected out of 1100

assign(segid A and resid 48 and name HD*)(segid B and resid 1 and name HH2) 3.5 2.0 2.5
SELRPN: 3 atoms have been selected out of 1100
SELRPN: 0 atoms have been selected out of 1100

Check the atom naming for those two restraints.

Further the restraint energy of your final models is rather low.