I am getting errors when attempting to submit PDBs to HADDOCK. I am attempting to dock some glycans to pilin and I can get neither the pilin nor the glycan pdb’s to parse. I’ve completely renumbered the residues and added in the correct chain ID.
For the pilin I’ve ended up with the following error (note the file is 14389 lines long and the entry to that line is END)
Error in PDB file.
Could not parse the PDB file at line 14389: record unknown ()
For the Glycan I’ve ended up with
Error in PDB file.
Issue when parsing the PDB file at line 1 .
ATOM/HETATM line does not meet the expected format
File in question’s first line is
HETATM 1 O1 GAL B 6 25.224 30.447 29.172 0.00 0.00 O
where as the example is
HETATM 9 C1 NAG B 102 171.992 99.750 236.168 1.00 10.00 C
I am quite stuck any help would be really appreciated.
The PDB format is very strict. Columns alignment is critical.
You could try to read it for example in PyMol and export it again (as PDB format).
Or try to validate your file using our PDB-tools web portal at:
https://bianca.science.uu.nl/pdbtools/
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Thanks, while manually editing I added a space between the Chain ID and Res ID as when the Res ID >= 1000 the two columns bleed into each other but it turns out that was not an issue so just using PDB-tools and not touching anything fixed the pilin.
Still having the same issues with my glycan it was just regularly exported from pymol and I renamed the Residue ID’s in accordance with
HADDOCK Web Server - Settings.
i.e changing ATOM /HETATM , 4YB/NAG/ , 3LB/GAL , 0SA/SIA.
I admit I made a slight blunder because I neglected two spaces so it was not quite right.
However now its telling me that because of NAG it should be ligand (and when i switch it to ligand it tells me to switch to glycan for the same reason)
There seems to be an issue with the submission of glycans at the moment, we will work on a fix!
@cfogarty, the issue should be fixed! Please try again. 
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PDB is parsed ! Thank you !
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Thanks !