Solar cells made from organic photovoltaic (OPV) materials have the potential to provide sustainable solar power generation due to their low manufacturing cost and processability. Molecular dynamics (MD) simulations allow for close examination of the behavior and properties of OPVs. The first step of simulating a new compound in MD is deciding how to apply force field parameters based on the chemical structure of the molecule, and if the chemical environment is not defined in the forcefield, then new parameters must be created. Here we develop and compare two computational tools for identifying bond, angle, and dihedral constraints that are missing from a forcefield, and perform quantum chemical calculations to parameterize these missing components. We set up the Espaloma and QUBEKit software stack on the Borah high performance computing (HPC) cluster, utilize SMILES strings to specify minimal molecular snippets, and parameterize models of Y6 and BTO, which have recently demonstrated power conversion efficiency over 17%. We perform MD simulations of BTO and Y6 across a range of densities and temperatures, and analyze structure using both real and frequency space techniques. We observe no evidence of crystal structures or other long-range periodicities, which suggests that these disordered morphologies have high charge transport despite their lack of order, in contrast to other OPV materials.