Problem with "no residues" and format file?


I started with HADDOCK docking and I have prepared my PDB in PyMol, but then this file is in format “PyMol Session file” - is that the reason why my HADDOCK has error and can´t be processed?

In received e-mail was this: “Exception: ERROR: PDB file /tmp/890982582.tmp contains no residues” (but I wrote numbers of residues in selected chain).

Thank you very much,


Hello Michaela,

Yes this is the reason. Pymol sessions are proper to PyMol and do contain many information that no other software than PyMol can handle. You need to provide a PDB file (see there for more information:

When you prepare your docking with PyMol, save each molecule you want to dock with the File > Save Molecule… option in the GUI or by typing the following command:

save my_molecule1.pdb, <molecule selection>

Thank you! Now it works well.