The absorption spectra of the cationic polythiophenes shift to the red, or the color changes in the solution are visible to the naked eye, when single-strand DNA (ssDNA) is added, so that they can be used as a tool for DNA detection, theranostic applications, and biological sensors. The red shift or color change is explained by the fact that the ssDNA leads to conformational changes in the polythiophene, but the form of structural change remains to be elusive (i.e. flattening, twisting, stacking, etc.). In this study, molecular dynamics (MD) simulations of complexes consisted by ssDNA sequences with different nucleotides and polythiophene containing cationic side group were performed to enlighten the experimental studies. For this purpose, force field parameters of polythiophene which are not present in the current databases, were generated. The interactions between them were analyzed to determine the nature of conformational changes in the polythiophene when ssDNA was added. MD simulations has been carried out with the CHARMM-compatible force field parameters obtained in the content of this work. Radius of gyration of oligomer increases with addition of ssDNA but is more affected by homopurine strand. Planarity index gets larger upon complexation with homopurine and T_rich strand, does not change with others. H-O and electrostatic interactions which are almost doubled in nonplanar complexes can be interpreted as the major sources of conformational changes in oligomer. Considering all types of interactions between atoms in duplexes, it was observed that planarity was high in structures with less interaction of oligomer side groups.