Article ID: 579 - Last Modified: June 7, 2011
I used the refine option in Glide for a series of analogues, which I expected to all produce results. However, two of the structures did not appear in the pose viewer file. What might the issue be?
It is likely that the grid is too small for these ligands. Try increasing the size of the grid box when you generate your grid so that it can accommodate the ligands. One way to do this is to include the largest of your ligands in the Workspace when you create the grid, and ensure that it is correctly positioned in the binding site. Then use the option to define the grid box size by picking the ligand and choosing the size option "Dock ligands similar in size to the Workspace ligand". Another alternative is to place the ligand in the Workspace and measure the distance between the most distant atoms, and use this distance to set the grid box size with the "Dock ligands with length <=" option.
Keywords: refine, flexible docking, poseview, score-in-place mode, GlideScores, Glide
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