Is there a way I can assign a free radical atom type for oxygen in the Build panel? I want to create a tyrosyl free radical.

There is no free radical MacroModel atom type for oxygen if you are looking for it in the Atom Properties tab of the Build panel under Atom type (MacroModel). The only option there is CR (12): carbon free radical. Most force fields don't treat free radicals as usually there are no parameters available for them.

However, you can easily build the free radical in Maestro: delete the hydrogen and make sure that the charge on oxygen is 0. If you plan to run QM calculations using Jaguar, then it doesn't matter what atom type you assign. As long as the molecular charge and spin multiplicity are specified correctly in the Jaguar panel, the molecule will be treated as a free radical. If you want to do a calculation on a protein, you can use QSite, and include the free radical in the QM region.

Keywords: free radical atom type, build , Maestro, QSite

Back to Search Results