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Questions and answers > MD simulations
do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Rajendra Kumar:
Hello,
As discussed in this thread (http://forum.x3dna.org/related-topics/wrapper-for-gromacs-md-trajectroy/), now, do_x3dna (https://github.com/rjdkmr/do_x3dna) package is available for download and installation.
I am still working on the Python-APIs, which enable the user to perform specific analysis. Soon, I will upload a extensive tutorial for using these APIs.
Any suggestions would be very helpful to improve this package.
Thanks.
With best regards,
Rajendra
Rajendra Kumar:
Hello,
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 (http://rjdkmr.github.io/do_x3dna/apidoc.html).
Few tutorials about the Python APIs are also now available (http://rjdkmr.github.io/do_x3dna/tutorial.html).
Thanks.
With best regards,
Rajendra
xiangjun:
Hi Rajendra,
Thanks! Your do_x3dna is quite impressive, especially the extensive documentation and tutorial.
Best regards,
Xiang-Jun
Rajendra Kumar:
Hello,
Now an application note is online for do_x3dna in Bioinformatics (http://bioinformatics.oxfordjournals.org/content/early/2015/04/01/bioinformatics.btv190.short).
If you are using do_x3dna tool, please cite both 3DNA and do_x3dna papers.
Thank you very much.
Hi Xiang-Jun, Thank you very much for your support.
With best regards,
Rajendra
xiangjun:
Hi Rajendra,
Congratulations! I wrote a short blog post on April 7, 2015 on the 3DNA homepage , titled "The do_x3dna paper by Kumar and Grubmuller in Bioinformatics", after noticing your do_x3dna publication online. I also read the paper and forwarded it to my colleagues.
Along with 3D-DART, there are now two known outside (w3DNA is the 'internal' one from the Olson lab) interfaces to the 3DNA Suite of programs. It is gratifying to see the widespread usage of 3DNA, and the trust the community puts on the software. I strive to ensure that 3DNA can be counted on in the years to come.
Best regards,
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
