Hello, I am trying to select grid values on autodock tools of my macromolecule but the grid points are not enough to cover my receptor, even if I max the spacing. how can i manage this issue.
Thank you in advance
Dear Margherita Vit , the grid box should cover the receptor if you max the spacing. Covering the whole receptor is required if In case you are trying to perform blind docking. If you know the catalytic site, you do not need to cover the whole receptor. covering the catalytic site with Grid box will be enough.
If you have details of binding/ active site residues covering it is good enough
If you're finding that the grid points generated by AutoDock Tools are not sufficient to cover your receptor, even with the maximum spacing, there are a few strategies you can try to address this issue:
1. Increase Grid Size: If the spacing is already at its maximum, you can try increasing the dimensions of the grid. This will expand the coverage area, potentially allowing more grid points to cover your receptor. However, keep in mind that increasing the grid size can also significantly increase computation time.
2. Adjust Receptor Size or Position: Sometimes adjusting the size or position of your receptor within the grid box can help ensure better coverage. You might try resizing or repositioning your receptor to better fit within the available grid space.
3. Grid Box Rotation: Experiment with rotating the grid box to align it more closely with your receptor. This can sometimes provide better coverage with fewer grid points.
4. Manual Editing: In some cases, you may need to manually add additional grid points using a different software tool or by directly editing the grid file. This can be more complex and time-consuming but may be necessary for precise control over grid placement.
5. Consider Different Software: If AutoDock Tools continues to be insufficient for your needs, you might consider using alternative molecular docking software that offers more flexibility and control over grid generation.
6. Contact Support: If you're still having trouble, consider reaching out to the support community for AutoDock Tools or the specific docking software you're using. They may be able to provide additional guidance or assistance tailored to your specific situation.
By trying out these strategies, you should be able to improve grid coverage for your receptor in AutoDock Tools.
Here is an open source PyMol plugin that can calculate gird box size based on the binding site.
And, the 'Docking with macrocycles' AutoDock vina tutorial may help:
https://autodock-vina.readthedocs.io/en/latest/docking_macrocycle.html
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