Can I implement the latest MARTINI version: 3.0.0 while implementing HADDOCK protein-protein docking? - essentially changing the ff parameters (itps), etc?
This is something on our to do list (in some future).
So you are welcome to try, but it might not be that simple.
And you can only do that in the local version of HADDOCK. Of course if you manage to do it, we can consider implementing it in the main version for a future release.