I always get this message ( Post-processing: FAILED (or skipped)) when I use unambiguous restrains TBL file. The job finishes successfully but in the end I find this message and also that my proteins were not docked.
This probably means that the restraints you provided are not matching the naming/numbering of your input PDBs and as such not used.
Which also explained why the proteins are not docked.
You can download the complete tar archive and check the naming/numbering/chainIDs of the generated PDBs against your restraints.
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The restrains I used : assign (segid B and resid 428 and name O2) (segid C and resid 169 and name C16) 11.67 3.9 12.3
B and C are the chain names. and I select them manually while I am uploading my PDB files in both menus the Chain and Segment id.
And I am getting the same result
Share the link to your run.
Did you name the two molecules chain B and C in the submission page?
Check a result PDB file, does it have those chain IDs? Are the residues present?
The link:
https://wenmr.science.uu.nl/haddock2.4/run/1368267329/74401-Distance-Ligand
The chains and the segments are named B and C in the submission page.
The residue is missing for chain C in the result PDB.
The residue is missing for chain C in the result PDB.
That explains the problem.
None of the files (even in the json file which contains your uploaded data) does residue 169 exist
Is it present in your original file?
Yes it is definitely in the original file.
The residue is a ligand, may this be the problem?
But also for chain B I am using a ligand residue
Unless you share the problematic PDB files we can’t do much - you can also email it
Kindly provide the email
Just for the record the fact that the run was failing was because of a wrong chain assignment of one of your ligands. I.e nothing wrong with the HADDOCK machinery.
The second problem comes from the fact your two proteins have different ligands, but you gave them the same residue name which is not a good idea since this will mess up the topology/parameter for those ligands. Each ligand should thus have a unique residue name.
And finally, by default HADDOCK uses chainID A for the first molecule and B for the second (can be changed with expert level access. Since your distance restraint is defined between chain B and C HADDOCK can not use it, which explain the failure to dock.
Thank you for the kind help