Ensemble dataset for "Unconventional DNA architecture in a dopamine–bound aptamer complex"

This dataset contains input and output files for the Amber system preparation and ensemble production for the publication "Unconventional DNA architecture in a dopamine–bound aptamer complex". It contains 6 zip files: system_prep.zip input: coordinates: input coordinates produced with Leap topologies: input topologies produced with Leap restraints: NMR-derived restraint file parameters: Amber input parameter files for all simulation steps 1_min: initial minimization step 2_heat: heating step 3_eq: equilibration steps ensemble.zip 4_prod_ensemble: production step for ensemble production out: output files trajectories restart files 5_min: final minimization step for ensemble production rmsd.zip. Pairwise RMSD values for the ensemble, replicated microsecond MD experiments, and unconstrained control for plotting. pca.zip. Scree plot and pca_values for plotting the comparative analysis of the 15 models in the ensemble. dssr.zip. DSSR analysis results for the ensemble hbonds.zip. Hbond data (distances and angles) and formation frequency for for plotting the formation of H-bonds over the course of the four restrained MD microsecond simulations, and the unrestrainted and no-dopamine controls. angles.zip. Dihedral and pucker angles for the restrained and unrestrained simulations, as well as the final ensemble. Microsecond MD experiment files are deposited at https://doi.org/10.5281/zenodo.18598398