Introduction

do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It consists of three main components:

do_x3dna — To calculate structural descriptors of DNA/RNA from MD trajectory. Also available as a stand-alone and independent VMD plugin.

dnaMD — Command line tool to extract and analyze the data obtained from do_x3dna for users without programming experiences.

dnaMD Python module — To extract and analyze the data obtained from do_x3dna for users with programming experiences.

Warning

DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge. This could be dowloaded from by 3DNA forum.

Last Update: Nov. 2023

For Questions and Discussions, please visit: do_x3dna forum.

Release Note 2023

do_x3dna can be compiled and used with GROMACS-2023.x versions.
Support for older GROMACS (4.5.x, 4.6.x, 5.0.x, 5.1.x, 2016.x and 2018.x) is removed.
For above listed GROMACS version, the code is available in 2018 git branch. Please use git checkout 2018 to use this version.

Release Note 2018

Added new dnaMD tools

Added support to calculate both global and local Elastic properties

Added tutorials to calculate elastic properties and deformation energy using dnaMD tool and dnaMD Python module.

Release Note 2017

do_x3dna can be compiled and used with GROMACS 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x versions.

do_x3dna VMD plugin

More user friendly — dnaMD tools to analyze do_x3dna data — No programming experiences needed now to analyze do_x3dna data.

Speed up dnaMD analysis with HDF5 file

Features

Base-pair parameters

Base-step parameters

Helical Base-step parameters

Major and minor grooves

Radius of DNA Helix

Backbone torsional angles

Example: Conformational wheel using backbone torsion angles:

Helical axis and its curvature

Examples:

Bending in the helical axis of a mitochondrial DNA:

Bending in the helical axis of a DNA in the nucleosome:

Citations

Please cite the following publications:

Xiang-Jun Lu & Wilma K. Olson (2003)

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

Nucleic Acids Res. 31(17), 5108-21.
Rajendra Kumar and Helmut Grubmüller (2015)

do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations

Bioinformatics (2015) 31 (15): 2583-2585.