We implement the higher order gyrokinetic theory developed in Dudkovskaia et al (2023 Plasma Phys. Control. Fusion65 045010), reduced to the limit of , where B0 is the tokamak equilibrium magnetic field, and Bϑ is its poloidal component, in the local gyrokinetic turbulence code, GS2. The principal motivation for this extension is to quantify the importance of neoclassical flows in electromagnetic gyrokinetics, with a particular interest in sharp pressure gradient regions where the bootstrap current becomes dominant. To incorporate neoclassical equilibrium physics, GS2 is coupled to NEO, a multi-species drift kinetic solver. It is found that the regions where microinstabilities are most likely to be influenced by neoclassical equilibrium effects are in a pedestal plasma and a spherical tokamak core plasma.