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Reducing van der Waals radius

2024-09-10
2024-09-12
  • Yutaro Hirono

    Yutaro Hirono - 2024-09-10

    Dear Dr. Koes,

    We would like to reduce the van der Waals radius of atoms in a fragmental moiety that are commonly found in our ligand molecules. Can I set up such calculations by using an option implemeted in smina ?

    Thank you in advance,

    Best regards,
    Yutaro.

     
  • David Koes

    David Koes - 2024-09-10

    --custom_atoms is what you want. To see the format of the file it is expecting run smina with --print_atom_types. If you are using the default Vina scoring function the number you want to change is the xs_radius.

     
  • Yutaro Hirono

    Yutaro Hirono - 2024-09-11

    Thank you very much for your quick reply! I will define new atom types and prepare the PDBQT files accordingly.

    Actually, the problem I am working on is the lack of docking poses where the common substructure of my ligands (the scaffold) is placed in the "correct" location. Is it possible to apply constraints on the positions of specific atoms in my ligands?

     
  • David Koes

    David Koes - 2024-09-11

    If you want to do template docking, I recommend generating a large ensemble of conformers for each of your ligands, aligning to the common substructure, and then minimizing with smina rather than docking.

     
  • Yutaro Hirono

    Yutaro Hirono - 2024-09-12

    Thank you for the very straightforward suggestion! I will try using --minimize, or --minimize --local_only. Does that sound appropriate?
    Additionally, is smina capable of performing such alignment? For now, I am going to use other software like RDKit.

     

    Last edit: Yutaro Hirono 2024-09-12

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