.cfg file for RNA-ligand docking

HADDOCK
1

Hello; I am trying to run Haddock in Linux to perform docking between RNA and a ligand. However, I do not know how to build a .cfg file to run Haddock with certain parameters.

I would be very grateful if somebody gave me some notions about how to build a .cfg file for this case. I have looked thorugh the .cfg files of the different examples but do not get to understand how to build one from scratch. Also, what files related to the RNA and the ligand do I need to generate for the docking to work?

Thank you very much!

2

I would take the protein-DNA example as a basis.

And it also depends on what kind of information you have to drive the docking.

And otherwise, simply use our haddock2.4 web server

3

PS: Especially since you are dealing with a ligand, you would have to provide topology and parameter files for your ligand.

The server does that automatically for you

4

Ok, thank you very much for your answer!