3DNA Forum

Questions and answers => MD simulations => Topic started by: Rajendra Kumar on July 09, 2014, 06:46:33 am

Title: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: Rajendra Kumar on July 09, 2014, 06:46:33 am: Hello,

As discussed in this thread (http://forum.x3dna.org/related-topics/wrapper-for-gromacs-md-trajectroy/ (http://forum.x3dna.org/related-topics/wrapper-for-gromacs-md-trajectroy/)), now, do_x3dna (https://github.com/rjdkmr/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
Title: Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: Rajendra Kumar on September 03, 2014, 10:53:31 am: Hello,

I have now made a new website for do_x3dna (http://rjdkmr.github.io/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 (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 (http://rjdkmr.github.io/do_x3dna/tutorial.html)).

Thanks.

With best regards,
Rajendra
Title: Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: xiangjun on September 03, 2014, 12:20:23 pm: Hi Rajendra,

Thanks! Your do_x3dna is quite impressive, especially the extensive documentation and tutorial.

Best regards,

Xiang-Jun
Title: Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: Rajendra Kumar on April 09, 2015, 06:28:49 am: 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
Title: Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: xiangjun on April 09, 2015, 10:15:48 am: 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 (http://x3dna.org/citations/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
Title: problem regarding installation of do_X3DNA
Post by: sacky0003 on June 17, 2017, 02:50:12 am: Dear users,

I have installed cmake-3.9, fftw-3.3.6,x3dna-v2.3.
But when I am trying to install do_X3DNA it shows error.
I have followed this steps:
1.tar xfz do_x3dna-master.tar.gz .... works fine
2. cd do_x3dna .....works fine
3.mkdir build .......works fine
4.cd build .......works fine
5.cmake .. -DGMX_PATH=/opt/gromacs -DCMAKE_INSTALL_PREFIX=/opt/do_x3dna .... errors occurred

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
LIBFFTW
linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBGMX
linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBGMXANA
linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src
LIBMD
linked by target "do_x3dna" in directory /home/saikat/gromacs/do_x3dna-master/src

-- Configuring incomplete, errors occurred!
See also "/home/saikat/gromacs/do_x3dna-master/build/CMakeFiles/CMakeOutput.log".

what should i do ?? help me out

Thanks and regards

Saikat
Title: Re: do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories
Post by: xiangjun on June 17, 2017, 09:59:56 am: The error message shows some variables (e.g., LIBFFTW etc) are not set. Presumably you need to install additional libraries, which are nevertheless not required by 3DNA per se. You may need to contact the author(s) of do_x3dna for further details.

Xiang-Jun