r/comp_chem • u/ehxcho • 3d ago

Standard method for moco

Hello everyone I'm currently studying how to dock Xanthine oxidase but I got stuck on vina not recognizing the Mo atom of the Xanthine Oxidase, is there any script or parameters I can use to make autodock vina accept my receptor. The workflow I'm currently doing is Pymol -- Meeko --- Autodock vina

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u/Bachurin 2d ago

I think you have only one option: Remove Mo, make a docking, then add manually Mo and perforfm long MD with complex and pray that ligand would properly reoriented. In some cases ones replaces glutamic or aspartic residues with Lysine to mimic positively charged area, but in your case it would be incorrect, I think.

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u/ehxcho 2d ago

Thank you for that sir, I'll consider this

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u/Alicecomma 2d ago

There are several Google hits that discuss this. Essentially, Autodock Vina has a fixed set of atoms it can deal with, and you have to recompile it from source with the right edits to have it recognize molybdenum. Autodock (non-Vina) allows you to add atom types without having to recompile.

There is other docking software that might handle your metal. Apparently MetalDock exists with Mo parameters. Someone may have an Autodock Vina recompile with molybdenum included.

Now, oxidases do tend to work with several metal cations in the active site - perhaps you can replace with calcium or a similar cation that is in the ADV atom set.

There's also the question of what you plan to do with the output. Oxidases can have as of yet unknown mechanisms, which makes any docking output alone kinda untrustworthy. No docking tool is gonna simulate the electron behaviour around a metal complex with changing oxidation state accurately. To confirm anything you'd be looking at QM/MM analyses involving a Mo(VI), Mo(V), and Mo(IV) complex. You're almost definitely gonna have to get used to recompiling software and building your own atom/bond parameter descriptions to get anywhere near a trustworthy answer in simulating those.

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u/ehxcho 2d ago

Thank you so much I'll consider this