[Chimera-users] Docking

[Greta Hodo]

Hi,
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 [cid:C2748141-718F-40C4-8964-A212C52FDB1A]

And this I how the molecule changes after the docking
[cid:C1EDE285-2873-437D-A034-5BB2D031BD67]
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!
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