Dear Haddock Community,
I encountered the following issue and was wondering if someone is able to provide some hints.
I was trying to reproduce an X-ray protein-ligand complex by redocking the ligand (in its crystallographic pose) to the protein using the template-based approach
I performed only water refinement dockings using the Haddock2.2 guru interface (following the guidelines here: Advanced refinement of molecular complexes – Bonvin Lab). Everything worked fine and I was able to reproduce the crystallographic binding pose.
However, I repeated some dockings with the Haddock2.4 interface and was observing different results, i.e. I was not able to reproduce the crystallographic binding pose whereas Haddock2.2 did! (following the guidelines here: Advanced refinement of molecular complexes – Bonvin Lab).
In addition to the above mentioned options I also changed some settings according to the recommendations within the ligand docking tutorial. This was done manually (Haddock2.2) or automatically by the new Haddock2.4 interface.
I compared both run.cns files but I did not detect any significant changes. Nevertheless, I repeated the docking with Haddock2.4 and adjusted those parameters. Unfortunately, I got the same result and was not able to reproduce results from Haddock2.2.
Later on, I had a more detailed look on respective docking poses and observed that in poses produced by Haddock2.4 more water molecules were placed within the binding pocket of the molecule. However, I was not able to figure out why.
Does anyone has some suggestions on how to adjust my parameters in order to reproduce the results from Haddock2.2 in Haddock2.4?
Thanks in advance for your feedback,