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…
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