Hi,
I have submitted my protein-DNA complex for refinement on HADDOCK2.4 web-server. I applied a point mutation on my protein, so for preventing clashes, I want to use HADDOCK. However, after refinement (I followed this protocol: Advanced refinement of molecular complexes – Bonvin Lab), the secondary structure of my protein looks distorted and my DNA molecule too.
Before, I used HADDOCK2.2 Guru interface for refinement of my complex, and it worked perfectly. Now, I guess HADDOCK2.2 is not available anymore (It gives Internal server error).
You can find my json file and input-output(cluster1_1) files in the attachment.
input.pdb (396.9 KB)
job_params.json (226.4 KB)
cluster1_1.pdb (277.6 KB)
Additionally, I tried to use Refinement interface on HADDOCK2.4 but it did not recognize the nucleotides at the end of the DNA. It gave error like this:
The following error occurred when processing one of your PDB file: Instances of ligand DA do not contain the same atoms
Do you have any suggestions for me?
Thanks in advance
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The problem comes from the ligand in your structure (should be defined as HETATM for submission to the server).
If you remove it the refinement interface does work. But of course you rather keep your ligand.
But currently there is an issue with ligands on the server… We are looking into it.
The ligand issue is solved. You can give it another try via the refinement interface, but make sure to define your SAM ligand at HETATM.
Thank you very much for your answer @amjjbonvin
I tried the Interface refinement but the error is still the same. I think that it is about DNA nucleotides (…Instances of ligand DA do not contain the same atoms).
Actually I am wondering that why HADDOCK2.4 submission does not work effectively. I guess it uses the same force field with HADDOCK2.2. Why the HADDOCK2.4 distorts my complex while HADDOCK2.2 preserved it?
Thanks in advance,
Kind regards
Actually I am wondering that why HADDOCK2.4 submission does not work effectively. I guess it uses the same force field with HADDOCK2.2. Why the HADDOCK2.4 distorts my complex while HADDOCK2.2 preserved it?
What are you exactly doing in both servers? Which parameters / options are you changing?
Also the DA error must be related to your input PDB.
When I tested after deleting the ligand it went through fine…
Can you share (again) the exact file you are submitting?
Actually for the 2.4 server we switched to the proper two letter code nomenclature (DA, DC, DG, DT).
If you use that, and in addition correct that one base is defined as HETATM, then the submission to the refinement interface of 2.4 does work.
The error message you were getting is however confusing.
Here is the file I just submitted and the corresponding json file.
Comparing the json file with yours, I see you did not define automatically restraints for the DNA.
input.pdb (213.9 KB)
job_params.json (232.2 KB)
And the refined model (no distortions that I can see):
cluster1_1.pdb (277.6 KB)
Hi,
Now, I switch the HETATM column of one DNA base, I can submit the whole complex to Refinement interface. Finally it is running. My new input file:
input.pdb (396.9 KB)
I hope that my output file will not be distorterd.
I think I did the same things in both servers because I followed your “Advanced refinement” protocols.
For 2.2 : Advanced refinement of molecular complexes – Bonvin Lab
For 2.4 : Advanced refinement of molecular complexes – Bonvin Lab
Thank you very much for your helps 
Good - and note that in your previous trials you did not turn on DNA restraints, which might be the cause of the problem.
If the current run is fine, compare the settings with your previous settings.