Peptide bonds break in HADDOCK 2.4

HADDOCK
1

Dear HADDOCK users,

I ran into a problem when using HADDOCK 2.4 to dock the interactions between arylomycin (a hexapeptide) and a signal peptidase of E. coli. In the result that HADDOCK gave me, the peptide bonds were broken and the arylomycin molecule was separated into amino acids and small segments, and they appear in different positions.
There are several unnatural amino acids in the ligand structure, which I set as HETATM in the pdb file. I’ve also uploaded the distance restraint file that assigned distance between ATOM and HETATM, as well as between each pair of HETATMs. I think the problem might have to do with my restraint file, but I don’t know what’s wrong.
Here’s a segment of my restraint file:

ASSIGN (segid C and resid 0 and name C1 )(segid C and resid 1 and name N ) 1.3 0.2 0.2
ASSIGN (segid C and resid 1 and name CN )(segid C and resid 1 and name N ) 1.5 0.2 0.2
ASSIGN (segid C and resid 1 and name CA )(segid C and resid 1 and name N ) 1.5 0.2 0.2
ASSIGN (segid C and resid 1 and name CA )(segid C and resid 1 and name CB ) 1.5 0.2 0.2
ASSIGN (segid C and resid 1 and name CB )(segid C and resid 1 and name OG ) 1.4 0.2 0.2
ASSIGN (segid C and resid 1 and name OG )(segid C and resid 1 and name H01 ) 1.0 0.2 0.2
ASSIGN (segid C and resid 1 and name CA )(segid C and resid 1 and name C ) 1.5 0.2 0.2
ASSIGN (segid C and resid 1 and name C )(segid C and resid 1 and name O ) 1.2 0.2 0.2
ASSIGN (segid C and resid 1 and name C )(segid C and resid 2 and name N ) 1.3 0.2 0.2
ASSIGN (segid C and resid 2 and name N )(segid C and resid 2 and name CA ) 1.5 0.2 0.2
ASSIGN (segid C and resid 2 and name N )(segid C and resid 2 and name H01 ) 1.0 0.2 0.2
ASSIGN (segid C and resid 2 and name CA )(segid C and resid 2 and name CB ) 1.5 0.2 0.2
ASSIGN (segid C and resid 2 and name CA )(segid C and resid 2 and name C ) 1.5 0.2 0.2
ASSIGN (segid C and resid 2 and name O )(segid C and resid 2 and name C ) 1.2 0.2 0.2
ASSIGN (segid C and resid 2 and name C )(segid C and resid 3 and name N ) 1.3 0.2 0.2
ASSIGN (segid C and resid 3 and name C )(segid C and resid 4 and name N ) 1.3 0.2 0.2
ASSIGN (segid C and resid 4 and name CN )(segid C and resid 4 and name N ) 1.5 0.2 0.2
ASSIGN (segid C and resid 4 and name CA )(segid C and resid 4 and name N ) 1.5 0.2 0.2

In which residue 0 is a N-terminal acetyl group, residues 1,2 and 4 are unnatural amino acids, and residue 3 is a glycine.

Please could you give me some advice? Many thanks!

2

Even when defining distance restraints between those atoms the peptide bond will be broken since the van der Waals interactions will prevent those short distances.
A covalent bond distance is shorter that what the van der Waals energy term allows.