[gmx-users] do_x3dna: A tool to analyze structural fluctuations of DNA/RNA during simulations

[rajendra kumar]

Dear G
ROMACS
users
,


I have developed do_x3dna <http://rjdkmr.github.io/do_x3dna/>
(http://rjdkmr.github.io/do_x3dna/)
for analysis of DNA/RNA during the molecular dynamics simulations. It uses 3DNA
package <http://x3dna.org/> to calculate several structural descriptors of
DNA/RNA from GROMACS MD trajectory. It executes 3DNA tools to calculate
these
descriptors and subsequently, extracts
and writes
descriptors
as a function of time
in text format files
.

do_x3dna generates
 several output files. For easy analysis of the obtained data, do_x3dna
package includes a Python
module
 dnaMD.py
<https://github.com/rjdkmr/do_x3dna/blob/master/Python_API/dnaMD.py>, which
contains several methods <http://rjdkmr.github.io/do_x3dna/apidoc.html> for
the analysis of
following
structural descriptors:

   - Base-pair parameters
   - Base-step parameters
   - Helical base-step parameters
   - Major and Minor grooves
   - H
   elix radi
   i

   - Backbone and Sugar dihedral angles
   - Helical axis and its curvature


Several detailed tutorials <http://rjdkmr.github.io/do_x3dna/tutorial.html>
are also provided for the dnaMD module.


With best regards,
Rajendra

-- 
|================================================|
|
* Rajendra Kumar                                       *|
| Max Planck Institute for Biophysical Chemistry
<http://www.mpibpc.mpg.de/english/start/index.php> |
| Theoretical and Computational Biophysics
<http://www.mpibpc.mpg.de/home/grubmueller/index.html>,      |
| Am Fassberg 11, 37077 Goettingen, Germany      |
| Tel.:  +49 551 201 2304                        |
|================================================|