Is there a way to perform a Glide calculation with water molecules? How do I take into account the possible movement of the water molecules?

With Glide, you can include water molecules in the grid if they are important to binding. Glide has other means of accounting for solvation effects, so waters are not needed for solvation.

Currently, the only way to take into account possible movement of the molecule would be to generate several receptor structures with different likely water orientations, create grids for each, and then dock your ligands to all the grids. If there are multiple crystal structures of your target with different bound ligands, that would be a good way to identify likely water orientations. You also could try a limited conformational search (e.g., with MacroModel).

Once you have multiple receptor/water conformations, you can use the Virtual Screening Workflow (VSW, on the Workflows menu) to generate the grids and perform ensemble docking, in which a ligand is ranked according to its best score among all the receptors to which it is docked.

Keywords: water conformations, movement , protein , Glide

Back to Search Results