Failed advanced refinemet


I am performing Advanced refinement on HADDOCK2.2 Multi-body interface server. I have 6 different states of the same system. My input pdb file formats are all the same but my 3 of runs failed in topology generation. I attached my pdb files here and tagged the failed pdb as “failed”. I am writing the error message below:

Status: FAILED There was an error in the topology generation. The most likely cause is an unusual format of your PDB structures.

I thought the error was due to clash in the structure, but also I though HADDOCK refinement will remove this clash. How can I solve this case?


cluster1-successful.pdb (398.5 KB)
cluster2-failed.pdb (398.5 KB)

May-be try first the HADDOCK2.4 refinement interface - it has several options for refinement.

Some of those are described in the following preprint:

Sure, but the reason of I am using HADDOCK2.2 is the output file includes the energy-per-residue (ene-residue.disp) file. In my previous runs, I could not find this file HADDOCK2.4 output.

Thank you

We have now added that option to the 2.4 refinement interface (needs expert/guru access).

Looking at your structure, the SAM ligand could the be problem…

And note that HADDOCK2.4 uses a different (PDB-like) nomenclature for nucleic acids.

It is very nice to hear that! But now in 2.4 refinement interface, I got this error:

The following error occurred when processing one of your PDB file: Instances of ligand DA do not contain the same atoms.

And now, I guess I solved the error on 2.2 server. I removed the hydrogens on structure and I submitted it. My status is “Running” now. :nerd_face:
Thank you for your all answers :slight_smile:

I think the 2.4 error is due to the P, OP1 and OP2 atoms.
And the 2.2 run give error again :confused:

Tweaked your PDB file. Deleted the SAM hydrogen atoms.
cluster2-failed.pdb (396.2 KB)

Seems working (so far):

Thank you @amjjbonvin
I am submitting my other runs by this way.