Currently, I’m using Vina to test putative docking sites generated by another program we are testing, our pipeline involves just automating the process of extracting atom coordinates and processing the receptor and ligand files prior to docking.
To speed up processing we use centroid coordinates for the gridbox from the putative ligand position and give an arbitrary size (usually not too much larger than the ligand being tested) For the grid box. My question is if the ligand is longer/bigger than the grid box, how does This affect Vina’s docking?
Attached is a docked result where we used a 20x20x20 grid box from the centroid coordinates (Predicted pose in blue and vina docked pose in pink) what are the conditions the Grid box sets for the docking. are there other ways to test the site without making the search space too large?
This will not effect your vina docking wheather the Ligand structure is longer/shorter ultimately have to bind with receptor anyway.
Grid box is set around the receptor's active pocket and it is not related to the ligand size.
Vina gives 9 poses, you can check the ligand conformation in each pose with the reported ligand conformation, and also compare the bond formations.
Christian Highfield check eboxsize. eBoxSize calculates an optimal box size for a query ligand in order to maximize the accuracy of molecular docking.
https://www.brylinski.org/eboxsize
https://github.com/michal-brylinski/eboxsize
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