In AutoDock, when I drag and drop the PDB file, the binding pocket appears correctly (which I also, confirm by PyMOL and Discovery Studio), but the grid box center (X, Y, Z) is set to (0.0, 0.0, 0.0). However, when I load the protein via Grid → Macromolecule → Open, the grid box moves to the center of the protein, not the binding site.
Omid Moradi
good. I suggest you to use molegro or castp applications to find the best binding site. the binding site contains 5 numbers: x center, y center, z center, x size, y size, z size. the center numbers indocate the center of bix geometry and size numbers indicates the volume of box in angestroms.
after you found the best active site you can add these numbers in autodock
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