The lowest energy of binding between 3-D of the selected protein or enzyme with the mode is prefer

Unlike Autodock Vina, Autodock 4.2 will return the exact number of binding poses set. To do so, just set the number of runs in the searching parameters tab as the number of poses wanted (In Autodock Tools, click on Docking > Search parameters > choose an algorithm > set the number of runs you want. For instance, number of GA runs while using genetic algorithm).

Vitor Rabelo, so do you mean that number of runs of algorithm is equal to number of poses generated? If so, what is the keyword in dpf file? (I prefer running AutoDock from command line or script.)

Anna Sekuła exactly. For example, you can change GA runs number directly in the DPF file by setting the desired number at the following line:

ga_run 10 # do this many hybrid GA-LS runs

Anna Sekuła not exactly :)

Number of runs (ga_run) defines what it says. The number of runs of the algorithm and it should be set to 50 at least. Preferably 100. Depends on Your system.

The number of poses You get is a different story. Two additional keywords influence this (analysis and rmstol). If You like running AD from command line (good choice btw) just look at the histogram in the resulting log file and there You have Your poses. In some cases with 100 runs it is still possible to get only 1 pose.

Marek Andrzej Wojciechowski, can you elaborate on these keywords? You say that they "influence" the number of poses, so you mean that you don't use them to set poses number explicitly?

No. You never know how many poses You are going to get. 100 runs may result in only 1 pose or even in 100 poses. "Analysis" keyword tells AD to cluster the results while "rmstol" defines how different two results can be to be still included in the same cluster/pose. So the same set of 100 results can be grouped in the small number of clusters when rmstol is large or ligand is not very flexible, or it can result in a large number of clusters when the opposite is true.