DNA/RNA molecular dynamics trajectory analysis with do_x3dna

With great pleasure, I read the following annoancement from Rajendra Kumar on the 3DNA Forum:

Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories 
« Reply #1 on: Today at 10:53:31 AM »


I have now made a new website for do_x3dna
(http://rjdkmr.github.io/do_x3dna). This website contains detailed
documentation for do_x3dna program and Python APIs.

Documentation for Python API is now available

Few tutorials about the Python APIs are also now available


With best regards,

Browsing through the do_x3dna website, I am impressed by the extensive documentation and tutorial. Clearly, do_x3dna has pushed the boundaries (in applicability and documentation) of the x3dna_ensemble Ruby script distributed with 3DNA v2.1.

As noted in GitHub page, do_x3dna has been developed to analyze fluctuations in DNA or RNA structures in molecular dynamics (MD) trajectories. It can be used for GROMACS MD trajectories, as well as those from NAMD and AMBER. It leaves no doubt that do_x3dna will boost 3DNA’s applications in the increasingly active field of DNA/RNA MD simulations.



I am getting error segmentation fault while running do_x3dna

— vishwambhar · 2016-10-02 03:39 · #


As mentioned in the post, do_x3dna was developed by Rajendra Kumar. You may be able to reach him in his GitHub mage. Sorry I cannot be of further help.

Good luck!

— Xiangjun · 2016-10-02 08:53 · #



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