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1. Why am I seeing a warning about the search space volume being over 27000 Angstrom^3?
This is probably because you intended to specify the search space sizes in "grid points" (0.375 Angstrom), as in AutoDock 4. The AutoDock Vina search space sizes are given in Angstroms instead. If you really intended to use an unusually large search space, you can ignore this warning, but note that the search algorithm's job may be harder. You may need to increase the value of the exhaustiveness to make up for it. This will lead to longer run time.
2. The bound conformation looks reasonable, except for the hydrogens. Why?
AutoDock Vina actually uses a united-atom scoring function, i.e. one that involves only the heavy atoms. Therefore, the positions of the hydrogens in the output are arbitrary. The hydrogens in the input file are used to decide which atoms can be hydrogen bond donors or acceptors though, so the correct protonation of the input structures is still important.
3. What does "exhaustiveness" really control, under the hood? （exhaustiveness为the number of runs ， 并行，可以设为cpu数，可以充分利用）
In the current implementation, the docking calculation consists of a number of independent runs, starting from random conformations. Each of these runs consists of a number of sequential steps. Each step involves a random perturbation of the conformation followed by a local optimization (using theBroyden-Fletcher-Goldfarb-Shanno algorithm ) and a selection in which the step is either accepted or not. Each local optimization involves many evaluations of the scoring function as well as its derivatives in the position-orientation-torsions coordinates. The number of evaluations in a local optimization is guided by convergence and other criteria. The number of steps in a run is determined heuristically, depending on the size and flexibility of the ligand and the flexible side chains.However, the number of runs is set by the exhaustiveness parameter.Since the individual runs are executed in parallel, where appropriate, exhaustiveness also limits the parallelism. Unlike in AutoDock 4, in AutoDock Vina, each run can produce several results: promising intermediate results are remembered. These are merged, refined, clustered and sorted automatically to produce the final result.
4. Why do I not get the correct bound conformation?
It can be any of a number of things:
If you are coming from AutoDock 4, a very common mistake is to specify the search space in "points" (0.375 Angstrom), instead of Angstroms.
Your ligand or receptor might not have been correctly protonated. （初始结构没有优化好）
Bad luck (the search algorithm could have found the correct conformation with good probability, but was simply unlucky). Try again with a different seed.
The minimum of the scoring function correponds to the correct conformation, but the search algorithm has trouble finding it. In this case, higher exhaustiveness or smaller search space should help. （搜索算法没有找到最优结构，可以增大exhaustiveness或减小search space）
The minimum of the scoring function simply is not where the correct conformation is. Trying over and over again will not help, but may occasionally give the right answer if two wrongs (inexact search and scoring) make a right. Docking is an approximate approach.
Related to the above, the culprit may also be the quality of the X-ray or NMR receptor structure.
If you are not doing redocking, i.e. using the correct induced fit shape of the receptor, perhaps the induced fit effects are large enough to affect the outcome of the docking experiment.（换受体结构）
The rings can only be rigid during docking. Perhaps they have the wrong conformation, affecting the outcome.
You are using a 2D (flat) ligand as input.
The actual bound conformation of the ligand may occasionally be different from what the X-ray or NMR structure shows.
Other problems

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