Project ID: plumID:22.037
Name: Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site
Archive: https://github.com/mrjoness/abasic-thermo/archive/refs/heads/main.zip
Category: chemistry
Keywords: metadynamics, DNA, abasic
PLUMED version: 2.7
Contributor: Mike Jones
Submitted on: 16 Oct 2022
Publication: B. Ashwood, M. S. Jones, A. L. Ferguson, A. Tokmakoff, Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site. Proceedings of the National Academy of Sciences. 120 (2023)
PLUMED input files
| File | Compatible with |
|---|---|
| metad_setup/11bp_abasic-2_plumed.dat |   |
| metad_setup/11bp_abasic-4_plumed.dat | |
| metad_setup/11bp_abasic-6_plumed.dat | |
| metad_setup/11bp_plumed.dat | |
Last tested: 22 Apr 2024, 20:51:17
Project description and instructions
Input files are compatible with the 3 Sites Per Nucleotide (3SPN.2) plugin for LAMMPS and applied to three 11-mer DNA oligomer sequences. 11bp_plumed.dat biases the mean distance between native base pairs for an intact (WT) oligomer. 11bp_abasic-6_plumed.dat biases the mean distance between all available native base pairs for an abasic sequence with the central nucleobase removed. PLUMED files for additional abasic configurations can be generated using abasic_site_to_plumed.py.
Submission history
[v1] 16 Oct 2022: original submission
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