Question: Why Grid centers are different between Glide and ADTvina for the same Ligand-protein structures
gravatar for maria2019
7 months ago by
maria2019130 wrote:

I am trying to conduct docking of couple of ligands on a protein using Glide and Autodock vina.

When I want to choose the same grid box using the co-crystalized ligand and protein with the 2 tools, I realize that glide and ADTvina give different Grid x,y,z center coordinates!! is that normal??

Since I want to do the docking with 2 tools and then choose the docked poses that are common between the two, I think it is better to set the same grid box size and coordinates. Or that is not really the case and I just need to chose the grid for each of the tools that gives the lowest re-docked pose RMSD compared to reference?

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