Problem with HADDOCK (multiple forms of the same residue)

Hi everyone,

I’m working on predicting protein-protein interaction (6YI3 of SARS-CoV and 1ZJK of MASP2) and cannot submit my job because of following error:

  • With the 1ZJK pdb file, it said:
    "Issue when parsing the PDB file at line 2743 .
    Your PDB contains multiple forms of the same residue MET 586 . This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble.

ATOM 2179 CE AMET A 586 13.656 -14.153 25.422 0.50 26.69 C (Offending Line) <–
ATOM 32 N ARG 3 11.281 86.699 94.383 0.50 35.88 N (Example Valid Line)"

  • I tried pdb_selaltloc.py but it didn’t work.

  • I used HADDOCK 2.4 server.

Please could you guys help me out with this. Many thanks for your time and kindness.

  • I tried pdb_selaltloc.py but it didn’t work.

Define “it didn’t work…”

You can also try our now pdbtools server at: wenmr.science.uu.nl/pdbtools

Thank you very much. It works.
By the way, when I submit the job, there is a missing residue in the fixed file (that I let it automatically added by HIS). Should I do it that way or manually modify it ?
Again, many thanks for your kind support.

By the way, when I submit the job, there is a missing residue in the fixed file

Be more specific if you want an answer…

What kind of residue?

I just figured out my problem. Many thanks for your help.