Error in the topology generation

Hello, I am submitting my own pdb files, and I get the following error:
Error in the topology generation: prot_psf_A could not be created

I removed all the HETATM from the pdb file, it ends up with END, doesnt have the segid.
What else could be wrong with that pdb?

Without seeing the PDB it can only be a guess but could it be that your PDB contains modified amino-acids ?
They are still labelled as “ATOM” but are not supported by HADDOCK (the list of modified amino-acid supported by HADDOCK is available here:

You can check the correct formatting of your PDB file using our script from our pdb-tools GitHub repository:

E.g.: <my-input-pdb>

It seems everything is OK.

I got this outcome :wink:

If this problem persists, do inspect the content of the generate_A.our file in the begin directory and start looking for error messages at the bottom of that file. Are you running a local version?

5098 %GENRES-ERR: residue TPO not found in topology files. Add topology definition.

Thank you!

In the list of modified amino acids supported by HADDOCK, you can find

TOP: phosphorylated THR.


So do change the name of that residue in your PDB file

hello there, I am submitting my own PDB files, one of them showing error during generation of .out files
%GENRES-ERR: residue UNK not found in topology files. Add topology definition.
But I want to do protein-protein docking with this drug bind to it.
Is there any possibility???


If you look at this page:
You’ll see that co-factors must be defined as HETATM to get their topologies obtained from PRODRG.

Using our web server?

Co-factors and small ligands should be defined as HETATM instead to ATOM

No, I am using software haddock2.2.
Can we modify the topology files?
Please help me in this regard!!!

The local version of HADDOCK is definitely not user-friendly, thus the existence of the web server. If you have 3-4 core developers telling you to use the server, you should listen. You haven’t given us a good reason as to why you want to use the local version.

If you want to add a new molecule/residue to the topology, you’re in for a lot of work. You need to use an external software that calculates exactly what the bonds, angles, partial charges, etc are. It’s not simple.

Please, do give another try to the webserver. You’re wasting your own time trying to fix all of these issues when you could be analyzing your runs…

Reading the online manual might also help…