Effect-of-Helicase-Separation-on-GC-Tautomerism

This repository contains the data and analysis presented in the article entitled "Proton Transfer During DNA Strand Separation as a Source of Mutagenic Guanine-Cytosine Tautomers".

Molecular dynamics files

The following files can be used to reproduce molecular dynamics files in Gromacs 2018 with the CHARMM36 and SPCE force fields:

• DNA14_rdy.gro (Solvated and neutralised double stranded DNA with 14 basepairs)
• min.mdp (minimisation control file)
• eq500ps_dna.mdp (equilibration NVT control file)
• md200ps_dna_pull90min.mdp (example SMD control file)

ML-NEB files

• long paths, paths longer than 2A separation distance
• paths, 0-9 ordered in increasing separation distance according to manuscript
• stacked, calculations on reaction path including stacking interactions