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Is 5Å big enough for your docking grid box?
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Recently, I am preparing a manual script for previous work. When someone read it he claimed in the email: "your gird box for docking is too small to include the whole molecule. I measure the distance between two atoms in the ligand and it is 11Å, but you defined your grid box as 5Å ...." Such statement really surprised me because I finished the docking in Schrodinger. When I define the grid box size, I definitely sure that the grid box is big enough to include the whole ligand for Glide grid box definition is visualized and it shouldn't be any reasons to make such mistakes.
I turned to the manual for grid box description, it is said the grid box axis is centered in ligand and the length is measured in radius. In other word, the diameter is 10Å and the diagonal for such grid box is 17.3Å . Obviously, such space is large enough for 11 Å.
https://blog.sciencenet.cn/blog-355217-443156.html
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