@JulioColl I have no hands-on experience with docking experiments in silico (nor in vitro). After installation of Vina and the GUI suggested by the video tutorial, AutoDockTools (I got version 1.5.6, Sep_17_14 to start), however, I noticed File -> Read Molecule accepts .mol2, .pdb, .cif as formats in addition to .pdbqt.

Since there is no explicit bond order information in the .pdbqt (well, the .cif doesn't either) I assume the program «somehow» recognizes and marks bonds as fix (e.g. the stilbene double bond) and others as conformational flexible (like C-C in an attached methyl group). Time to replicate their tutorial.