I am working on protein-ligand docking. i have successfully completed the run but now i have a doubt on the analysis part. in the results, i have a folder called structures under which there are two subfolders it0, it1 and further inside it1 i have a water folder. Each of these folders contain certain energy results. I am quite confused as on to check which folder for my result. Though i understand what each of these folder means, but still am not quite clear to pick which one i should choose for my further studies. It would be really helpful if someone can provide me a clear difference between these folders…
It is probably time to start reading some of our HADDOCK papers that describe the entire protocol.
and more to be found on our publications web page at: http://www.bonvinlab.org/publications/
Some are protocols published in the Methods in Molecular Biology series.
Further the online manual described the various docking stage. See:
it0: contains rigid body docking models
it1: flexible refinement models
water: the final, water-refined models and those are the ones used in the server results page