Ensemble docking pdb file with multiple chains

HADDOCK
1

Hello everyone,

I have the following problem while using the webserver: I would like to dock 2 proteins (each pdb file contains 35 states, representing changes in conformations that resulted from MD simulations).

The error that I am encountering is First pdb file contains multiple chains with overlapping numbering:. The solution provided for this is to renumber each chain so that there is no overlap.

However, how could one define the residues that participate in the interaction, for example, if each chain will have shifted numbers? Should I define a separate comma-separated list for each chain?

Is there any elegant (or not so elegant) way to solve this problem?

Many thanks!

2

Does the first molecule consist of multiple chains?

If not then most likely there is a problem in the way you generated the PDB file containing your ensemble of conformations.

You can use our PDB-Tools for that (e.g. pdb_mkensemble) to ensure a correct format.

3

Yes, the first molecule consists of multiple chains, each chain representing one state of the MD ensemble. (the same in the case of the second one).
LE: I should also mention that the first pdb file is quite big, exceeding the 99.999 atoms limit of pdb_tidy

4

I think you are wrong in your description:

Your first molecule seems rather to consist of a single chain, but you have various conformations extracted from your MD.
As such each conformation should have the same chainID and the conformations should be combined into one PDB ensemble with MODEL / ENDMDL statements distinguishing the various conformations, as in done to represent NMR ensembles in PDB entries.

Again, such a file can be generated with our PDB-tools from the ensemble of separate PDB files for the various conformations.

5

Thank you for your reply, dr. Bonvin! Will reformat it and resubmit. Hopefully it will work.