I am working on a system in which the ligand forms a dimer. Can I dock ligand dimers with Glide ?

Glide can only dock single molecules. However, if you have a dimer, you could join the two monomers with zero-order bonds, and Glide will treat the dimer as if it were a single molecule. The zero-order bonds are not treated as rotatable, so you would have to ensure that you had a good dimer geometry before adding the zero-order bonds and docking the molecule. You might for example want to run a minimization and conformation search on the dimer with MacroModel first.

An alternative would be to run a minimization and conformation search on the dimer with MacroModel, then position it in the receptor and do a second minimization or conformational search to find low-energy binding modes. You can then evaluate a binding energy with Prime MM-GBSA or Embrace. This approach might be preferable if the dimer geometry differs significantly in the binding site from the free state, e.g. if the dimer is only weakly bound when it is not attached to the receptor.

Keywords: docking, dimers, Glide

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