Problem with "no residues" and format file?

HADDOCK
1

Hello,

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,

Michaela.

2

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: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).

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>

3

Thank you! Now it works well.