Article ID: 207 - Last Modified: December 4, 2010
When I perform a docking job that uses flexible hydroxyl groups on the receptor, what receptor conformational states are used, and how much longer will it take my calculation to run? How can I set up such a calculation?
When you use flexible hydroxyl groups, Glide will position each sampled hydroxyl in each of its rotameric minima. There are always two or three positions that are sampled, depending on the residue. For example, tyrosine has two possible OH positions and serine has three possible OH positions.
The effect on docking times will depend on the docking mode you use. For example, with Glide SP, calculations with 8 flexible OH groups would take about twice as long as calculations with no flexible OH groups. With Glide XP, simulations that use N flexible hydroxyl groups will take N times as long.
However, both of these timings are much better than the time required to run all possible combinations of flexible OH positions. This is true even for XP — although you may use four flexible hydroxyls, if there are two rotational minima for each OH group, that represents 16 (24) possible receptor conformations.
To set up such a calculation, use the "Rotatable Groups" tab of the Glide Grid Generation interface (Applications → Glide → Grid Generation). Simply choose the residues whose hydroxyl positions you wish to sample, and run the grid generation calculation. Docking calculations that use these grid files will automatically sample the hydroxyl torsions you specified earlier.
Keywords: Glide, flexible receptor, rotatable, rotation, hydroxyl, hydroxyl rotation, rotatable groups, Maestro
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