Ligand minimization

Scoring and Minimization with AutoDock Vina

Status: Beta

Brought to you by: dkoes

Ligand minimization

Forum: Help and Feedback

Creator: Sherif Elsabbagh

Created: 2024-03-21

Updated: 2024-03-21

Sherif Elsabbagh - 2024-03-21

I know this might be a very basic question. But I need to make sure.

Before using smina, is it really necessary to minimize ligands ? Because I read somewhere else a comment saying that ligand energy minimization is not that necessary

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David Koes - 2024-03-21

smina only samples torsions. If there are issues with the rest of the geometry they will not be fixed. Pretty much any conformer generator will produce reasonable conformations that do not need additional energy minimization.

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Sherif Elsabbagh - 2024-03-21

thanks so much..

because I always use open babel to generate 3D conformer with --minimize .. but someone mentioned that you do not need this. just convert to 3D..

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