SI_October2023.pdf contains:

• A discussion of accounting for the finite size of the periodic simulation box
• Figures with the vertical energy gap distributions
• Tables with the RMSFs of DNA residues belonging in the QM region of all systems
• Tables with the identified DNA-protein close contacts
• Table of average hydrogen-bonding interactions with the defect regions and solvent molecules
• Table of average hydrogen-bonding eligible partners with the central base of the QM region and solvent molecules
• Table of the number of average solvent oxygen atoms within 3.5 Å of the N7 atom of the central base
• All 41 structural parameter distribution plots as well as select section-by-section structural parameter plots
• Tables of structural parameter means, standard deviations and selected Z-scores
• RMSF plots of base flexibility for four DNA sections
• DNA-water radial distribution functions for the phosphorus atoms of the DNA backbone near the quantum region and oxygen atoms in water

analysis directory contains:

• counting_protein_contacts.f90 : to calculate number of strong protein-DNA interactions
• curves_scripts
• • curves_plots.ipynb : jupyter notebook to generate paramter distributions and statistics
  • curves_run_and_process_scripts
  • README exaplaining how to use the curves processing scripts in curves_run_and_process_scripts directory
• gromacs_hbond_readme : short description of how to count hydrogen bonds for classical MD trajectories
• rmsf_notebook.ipynb : jupyter notebook to generate rmsf plots
• vertical_energy_gap_scripts to calculate energy differences between oxidized and reduced systems with the same coordinates
• • calc_gap.f90 (and affiliated .o file)
  • calc_gap_half.f90 (and affiliated .o file)
  • de_distr.f90 (and affiliated .o file)

classical_MD directory contains:

• N.B. Full trajectory files are too large for github or zenodo storage, so reduced, representative trajectory frames (every 500 time steps) are located directly on zenodo
• 8oxoG_reg1 directory
  • 8oxoG_oxidized_reg1
    • • wt_ox_reg1_mdrun.mdp : production run input for gromacs classical MD
    • wt_ox_reg1_structure.gro : strucutre input for gromacs classical MD
    • wt_ox_reg1_topology directory with all topology itp and top files
  • 8oxoG_reduced_reg1 : analogous to above
• 8oxoG_reg2 directory
  • 8oxoG_oxidized_reg2 : analogous to above
  • 8oxoG_reduced_reg2 : analogous to above
• rmsf directory contains section-by-section rmsf values by system resid
• wildtype directory
  • wt_oxidized_reg1 : analogous to above
  • wt_oxidized_reg2 : analogous to above
  • wt_reduced_both : analogous to above

curves_runs directory contains:

• run_curves.sh : input run file for CURVES+
• 8oxoG_0_reg1_curves_data : csv files of all curves parameters (no DNA tails full csv, by section csv)
• 8oxoG_0_reg2_curves_data : analogous to above
• wt_0_curves_data : analogous to above

QMMM_MD directory contains:

• N.B. Full trajectory files are too large for github or zenodo storage, so reduced initial trajectory frames are found directly on zenodo. There are 60 frames from the first 60000 time steps of each trajectory.
• 8oxoG_reg1
• • 8oxoG_reg1_oxidized_qmmm
  • • cpmd.inp : input file for cpmd qmmmm md run
    • gromos.g96 : classical gromos structure input
    • gromos.inp : gromos input for classical mm part of qmmmm run
    • gromos.top : gromos topology
    • starting_structure.g96 : starting structure in g96 format
• • 8oxoG_reg1_reduced_qmmm : analogous to above
• 8oxoG_reg2
• • 8oxoG_reg2_oxidized_qmmm : analogous to above
• • 8oxoG_reg2_reduced_qmmm : analogous to above
• wt_reg1
• • wt_reg1_oxidized_qmmm : analogous to above
• • wt_reg1_reduced_qmmm : analogous to above
• wt_reg2
• • wt_reg2_oxidized_qmmm : analogous to above
• • wt_reg2_reduced_qmmm : analogous to above
• water_qmmm_N7 : Raw data of solvent oxygen atoms within 3.5 Å of the N7 atom of the central base at any point within the QM/MM MD trajectories

wfn_optimization directory contains:

• wf_1.inp : example CPMD input for performing a wavefunction optimization for oxidized quantum region
• wf_0.inp : example CPMD input for performing a wavefunction optimization for reduced quantum region