I have a problem with the result of autodock Vina. When I load a molecule in “mol2” format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? 

I attach the photo of the real molecule

And this I how the molecule changes after the docking 

The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in “mol2” format and “pdb” format

Hope you can help me!