Bonds missing in begin file

I’m trying to run 3 different starting positions of peptides with a protein.
my structure.list files looks like this:
and all the pdb structures put in are correct.

However, when I start to run haddock some of the peptides in the begin files are missing bonds when I open them In pymol. This never happened to me before.
I checked the measurement between the atoms and they are larger than in the original pdb structure, is this because I defined the atoms as flexible? still it’s weird that the bonds don’t show.
attached is a screenshot of how the peptide structure looks like in pymol


Please be more specific about what you mean by missing bonds

And check if this is still the case after the end of the run

As you can see in the figure, not all the lines are solid, but all the atoms are in the PDB file.
in it0 some of the docking results have this problem too, but from it1 none of them have this problem (maybe its because the energies are too high so they weren’t picked for the next step)

No special residues in your peptides?

Can’t help much without getting our hands on your models…

Did you try submitting to the server?

No special residues
how can I send it to you? Can I send you the files?
I put it in the server when all peptides are in one PDB file with different MDL numbers, but the best results that are shown will not be with the missing bonds anyway.

Then most likely it is a display issue at the begin stage…

You can email me the files if you wish.