In partially ordered organic semiconductors, the characteristic times of nuclear motion are comparable to those of charge carrier dynamics. It is impossible to describe charge transport using either static disorder models or temperature averaged electronic Hamiltonians. We build a model Hamiltonian which allows the study of charge transport whenever carrier and nuclear dynamics are not easily separable. Performing nanoseconds long molecular dynamics of a columnar mesophase of a discotic liquid crystal and evaluating electronic couplings, we identify realistic parameters of the Hamiltonian. All modes which are coupled to the electron dynamics can be described in the model Hamiltonian by a limited number of Langevin oscillators. This method can be applied to systems with both slow (nanoseconds) and fast (hundreds of femtoseconds) nuclear motions, i.e., with both dynamic and static disorder.