HADDOCK Restraints TBL file for crosslinks

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

I am attempting a model of a full length protein structure using two individually solved domain structures and crosslinking data. I am attempting to build my restraints file using example files I have found, but I am hoping someone can tell me what the values in the file mean. Specifically the the last three values following the chain, residue, and atom name values. Here is a few lines from what I have so far. Also, if someone could call me out if there are any obvious issues with it currently, I would appreciate it.

Thanks!

assign (resid 4 and name NZ and segid A)(resid 130 and name NZ and segid A) 21.7 0.1 0.1
assign (resid 93 and name NZ and segid A)(resid 130 and name NZ and segid A) 21.7 0.1 0.1
assign (resid 93 and name NZ and segid A)(resid 123 and name NZ and segid A) 21.7 0.1 0.1
assign (resid 106 and name NZ and segid A)(resid 123 and name NZ and segid A) 21.7 0.1 0.1

2

The two selections should have different segid’s if you want to define an intermolecular cross-link.

HADDOCK will use different segid’s for each molecule (by default, A, B, C … for molecules 1, 2, 3, …

As for the meaning of the last three numbers, there are:

1) the target distance
2) the lower bound correction
3) the upper bound correction

The distance range is thus between the minimum distance defined by 1 - 3 and the upper limit defined by 1 + 3

For cross-links 0.1 is clearly a bad choice… Those can be much shorted than the maximal distance.

All this is explained in our MS-cross link tutorial at HADDOCK2.4 tutorial for the use of MS crosslink data to guide docking – Bonvin Lab

Cheers
Alexandre