A method includes generating a nominal dose distribution based on an image and clinical goals. The method further includes generating a setup error dose distribution based on range and setup uncertainties. The method further includes generating a dose distribution for a parameter of an internal organ. The method further includes optimizing a planned dose distribution of an intensity modulated proton therapy plan by minimizing a total objective value including the nominal dose distribution, the setup error dose distribution dose distribution, and the dose distribution for the internal organ. The method further includes generating a final dose distribution for the intensity modulated proton therapy plan based on beam parameters of the optimized planned dose distribution. The method further includes controlling a proton therapy apparatus configured to deliver proton therapy based on the intensity modulated proton therapy plan with the optimized planned dose distribution.