Gold nanorods have interesting optical properties due to surface plasmon resonance effects. A variety of biomedical applications of these particles have been envisaged and feasibilities demonstrated in imaging, sensing, and therapy based on the interactions of light with these particles. In order to correctly interpret experimental data and tailor the nanorods and their environments for optimal use in these applications, simulations of the optical properties of the particles under various conditions are essential. Of various numerical methods available, the discrete dipole approximation (DDA) approach implemented in the publicly available DDSCAT code is a powerful method that had proved popular for studying gold nanorods. However, there is as yet no universal agreement on the shape used to represent the nanorods and on the dielectric function of gold required for the simulations. We systematically study the influence of these parameters on simulated results. We find large variations in the position of plasmon resonance peaks, their amplitudes, and shapes of the spectra depending on the choice of the parameters. We discuss these in the light of experimental optical extinction spectra of gold nanorods synthesized in our laboratory. We show that much care should be taken and prudence applied before DDA results be used to interpret experimental data and to help characterize nanoparticles synthesized.