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I’ve tried to use the prediction interface to predict the protein-protein docking but I received the results which do not have docking results but rather all the chains are scattered all over the place (7 from receptor structure and 1 from ligand protein).
Does anyone know what is the problem with it?
Thank you for the support
Download the tar archive of the run and look into the begin dir to see if this is already happening at the initial stage prior to docking. This would indicate a problem with your starting model.
And just to be sure, when you refer to the prediction interface you are referring to the HADDOCK web server, right?
Thank you for the support but when I checked the files in the begin dir, there were no problems with the initial stage. And yes, I’m using the prediction interface provided in HADDOCK web server.
Just in case, I’ve also checked the files in structures dir, and it seems like the scattering happened from it1 because I found proper structures in it0. Is there any way to know what is the problem and possible solution based on this information???
This is very strange… It could be that your protein model has clashes and the structure is exploding once you include the intramolecular interactions during it1…
It might not be the absolute answer and I should try with other structures if it also works with it but when I nominate the 7 chains in the receptor structure into one single chain, 7 chains from receptor did not scattered all over the place and successfully processed the protein-protein docking.