I wrote you a big message a week ago, but it was not posted. Probably, moderator decided it's too long.
Shortly, I follow instructions of videotutorial by Oleg Trott, one of the vina authors.
Regarding the question " Why I reopen pdbqt file" . I reopen it to be sure the partitial charges were assigned rightly, and I sow they were not.
Seems, Douglas is partially right. In the Autodock Vina FAQs I found the following.
Why don't the results change when I change the partial charges?
AutoDock Vina ignores the user-supplied partial charges. It has its own way of dealing with the electrostatic interactions through the hydrophobic and the hydrogen bonding terms. See the original publication [*] for details of the scoring function.
Then, I do not understand why vina requires pdbqt files as input, but not simply pdb ?
Thank you, all who took part in the discussion,