Geometric defects in conjugated polymers play a critical role in determining electronic structure and properties such as charge carrier mobility and band gap. Because the relative roles of individual defects are experimentally difficult to discern, computational approaches provide valuable insight if appropriate molecular models are used. Poly(3-alkylthiophenes) are often modeled with very short backbones and without their side chains. We demonstrate the shortcomings of this approach for modeling torsional disorder in poly(3-hexylthiophene) (P3HT). Using a hybrid density functional model, we identify a minimal acceptable model to comprise approximately 10 monomers with explicitly treated alkane side chains. Potential applications of this work extend to polymer electronics and optoelectronics.