Issue with breakaway of aminoacids

I used HADDOCK to dock protein(but speifically his analogue) to receptor and my issue is that the protein is like “chopped” - I mean: some aminoacids are chosen away from seqeunce and strewed around structure (in PyMol viewer). Do you know what is the issue, that these aminoacid act like this, please? In undocked protein is this sequence normal. They are 3 aminoacids on the end of chain a it one of them (and first of them) is derivated aminoacid - if this information helps.
Thank you.

Most likely your problem comes from the modified amino acids in your sequence.
Check the list of supported modified amino acids (and their proper naming):

Those supported amino acids should be defined as ATOM and not HETATM in the PDB file.

Thank you very much!