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