Thank you for the answer. I certainly understand the flexibility constraints in the pdbqt (which I made thinking of the complex as a rigid molecule). I'm understanding that this "bonds" don't actually matter (I'm right?), but the thing is if what I'm seeing with ADT is what Vina interprets too, and if that "bonds" (generated between the metal and the chelating agent in ADT, but not in other viewers like PyMol) matter for the docking itself.
Vina only sees what's in the PDBQT, and PDBQT does not contain explicit info about the covalent bonds. These need to be inferred by Vina. The inferred bonds may
be important in docking, as my previous message was trying to detail. However, the procedures used for inferring the bonds in Vina are unrelated to those used in PMV.
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