After applying FlexPepDocking, I got a silent output file. Then, I use cluster command to cluster the result files. Although the program gives the structure of each group, it is still difficult to decide which structure I should choose for further analysis. For me, I want the following statistics of the clustering result:
1.Sorting the binding energy of the structures in each group.
2.Binding Energy of each structure, so I can plot an “Energy-structure index” graph to decide how many structures I should consider for each group.