How to add the exclude volume?

Scoring and Minimization with AutoDock Vina

Status: Beta

Brought to you by: dkoes

How to add the exclude volume?

Forum: Help and Feedback

Creator: Xu Youjun

Created: 2022-02-16

Updated: 2022-04-23

Xu Youjun - 2022-02-16

Hello,

When I dock a molecule into the binding site, I just want to add a region with the exclusion volume. A sphere is a center with a radius, where the docking molecule would keep a vdw distance to. I would like to know how could I implement this function? Or any suggestions? Thanks

Best,

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David Koes - 2022-02-16

Put receptor atoms there.

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Xu Youjun - 2022-04-23

Yeah, it works. But I tried different atom types, and it return slightly diffrent energy values. I don't know which type is suitable for representing the property of the exclusion volume.

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David Koes - 2022-04-23

There's no atom type that only participates in repulsion but not van der wals so you aren't going to be able to get exactly what you want.

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Xu Youjun - 2022-04-23

Okay, I see. Thank you

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