After generating some 500 structure using nstruct command and looking the top 5% out of those structures revealed that for all the structures the phosphate ion binds to the same location . I found this quite strange, as far as I know docking searches the entire protein for interaction. To my surprise I found that in all the 500 structures generated , phosphate ion binds to the same location …
is it due to the following parametrs that I gave during docking :-
-start_from -1.731 32.589 -5.039
start_from position I copied from the tutorial. Exactly what should be this location when we don’t know the binding site, as in case of blind docking .
You said that I need to generate “ten runs each with -nstruct 500,”, what does this means. As I gave -nstruct 500 which generated the same no. of structures. Pls clarify this ??
How do I have to use the plot_funnels.R . Do I have to install the R package for this ??