.. |3DNA package| raw:: html
3DNA package
How to use GROMACS do_x3dna ?
=============================
It is the wrapper tool, which uses |3DNA package| to calculate several structural
descriptors of DNA/RNA from the GROMACS MD trajectory. It executes 3DNA tools to
calculate these descriptors and subsequently, extracts these output and saves in to
external `output files `_
as a function of time.
.. warning::
DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge.
This could be dowloaded from by `3DNA forum `_.
* ``do_x3dna`` tool can be used with trajectory file generated by any Gromacs version.
However, **tpr** file is supported depending on the version (either 4.5.x or 4.6.x
or 5.0.x or 5.1.x or 2016.x) used during the installation.
* In case of other versions or other programs such as NAMD and AMBER, **PDB** file
can be used in place of **tpr** file.
* Trajectories from NAMD and AMBER should be converted to Gromacs compatible formats such as trr, xtc, pdb etc.
**Execute following command to get full help**
::
do_x3dna -h
.. note::
To execute do_x3dna, |3DNA package| should be installed and ``$X3DNA`` environment variable (Detail is given in 3DNA manual) should be defined.
.. warning::
Before running do_x3dna, make sure 3DNA package is correctly working for the input DNA/RNA structure.
To check it, run do_x3dna with a input gro/pdb file containing only one frame instead of xtc/trr trajectory
file as follows: ::
do_x3dna -s topol.tpr -f check.gro -n index.ndx -noisy
``-noisy`` option enables the display of output messages raised by 3DNA tools
(``find_pair`` and ``analyze``), and these messages would be necessary to troubleshoot
problems related to the 3DNA package. Most common problem is the mismatch of residue names
in input DNA/RNA structure and 3DNA package dictionary.
.. warning::
Only PBC corrected trajectory and tpr files should be used as inputs. PBC corrected
PDB/GRO file can be used in place of tpr file. Index file **SHOULD BE** used to
select ONLY DNA/RNA in the input trajectory file.
Options
-------
::
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-o BP_count.xvg Output xvgr/xmgr file
-map BP_map.xpm Output, Opt. X PixMap compatible matrix file
-g map.log Output, Opt. Log file
Option Type Value Description
------------------------------------------------------
-[no]h bool yes Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]noisy bool no Generate information from the X3DNA package
-[no]hbond bool no Hydrogen bond map for base pairs
-[no]ref bool no Base pair parameters will be calculated from base pair of the reference frame
-name string g Output file names will be suffixed by this word after "_"
-[no]fit bool yes Fitting frames on reference structure
-[no]mwa bool yes Mass weighted fitting
-[no]lbpm bool no To calculate local base pair parameters
-[no]lbpsm bool no To calculate local base-pair step parameters
-[no]lbphm bool no To calculate local base-pair helical parameters
-[no]avg bool yes Average and Standard Deviation over all the frames
-[no]c bool no Output structural parameters between helical regions ("----" by default). It will invoke "-c" option with 3DNA analyze command.
``-ref``
~~~~~~~~
If ``-ref`` option is used, all structural descriptors are calculated on the basis
of the structure of the DNA/RNA present in the input tpr/pdb file, which is provided
with ``-s`` option. ``-ref`` option **SHOULD BE** used if output files are further
used as input files in `dnaMD `_ or `dnaMD module `_.
To analyze the formation or breaking of base-pairs during MD simulations, either ``-noref``
could be used or do not include ``-ref`` option because this option is switched-off by default.
``-fit``
~~~~~~~~
If ``-fit`` is enabled, the structure of DNA/RNA is fitted on the reference structure,
which is provided with ``-s`` option. During fitting procedure, DNA/RNA is translated
to origin such that its center of mass is located at the origin. Most of the parameters
are unaffected by this fitting procedure, however co-ordinates of the local helical axis
could mismatch with the input structure of the DNA/RNA.
``-hbond``
~~~~~~~~~~
To extracts hydrogen bonds for each base pair. A map.log ( ``-g`` ) file
is generated containing the base pair information as per index of the hydrogen
bond map ( ``-map`` ).
``-lbpm``
~~~~~~~~~
To calculate Local Base Pair Parameters (Shear, Stretch, Stagger, Buckle, Propeller
and Opening) with function of time, and average (with ``-avg`` ) of these parameters
with function of the base-pairs. ``-lbpm`` option calculates Local Base Pair Parameters
(Shear, Stretch, Stagger, Buckle, Propeller and Opening) with function of time, and
average (with ``-avg`` ) of these parameters with function of the base-pairs.
``-lbpsm``
~~~~~~~~~~
To calculate Local Base Pair-Step Parameters (Shift, Slide, Rise, Tilt, Roll and
Twist) with function of time, and average (with ``-avg`` ) of these parameters with
function of the base-steps. ``-lbpsm`` option calculates Local Base Pair-Step Parameters
(Shift, Slide, Rise, Tilt, Roll and Twist) with function of time, and average (with ``-avg`` )
of these parameters with function of the base-steps.
``-lbphm``
~~~~~~~~~~
To calculate Local Base Pair-Helical Parameters (X-displacement, Y-displacement,
H-rise, Inclination, Tip and H-twist) with function of time, and average (with ``-avg`` )
of these parameters with function of the base-steps. ``-lbphm`` option calculates
Local Base Pair-Helical Parameters (X-displacement, Y-displacement, H-rise, Inclination,
Tip and H-twist) with function of time, and average (with ``-avg`` ) of these parameters
with function of the base-steps.
``-c``
~~~~~~
3DNA generates outputs for base-pairs/steps that form the double-helix. However, some nucleotides
might not be the part of the double helix. To calculate of these mis-matched nucleotides, ``-c``
option can be used.
.. note::
Apart from the above parameters, following parameters are calculated using 3DNA package
for each frame and written in separate files as a function of time.
* local helical axis
* major and minor grooves
* local helical radius
* backbone dihedral angles (``alpha``, ``beta``, ``gamma``, ``delta``, ``epsilon``, ``zeta`` and ``chi``)
* sugar dihedral angles (``v0``, ``v1``, ``v2``, ``v3`` and ``v4``)
These files are listed below.
Output Files
------------
Following files are generated from ``do_x3dna`` with and without options:
.. list-table:: List of output files from do_x3dna
:widths: 1, 4
:header-rows: 1
:name: output-files-table
* - File name
- Output contents
* - base_pairs_g.dat
- Base-pairs
* - h-bond_g.dat
- Hydrogen bonds between base-pairs
* - L-BP_g.dat
- Base-pairs parameters
* - L-BPS_g.dat
- Base-steps parameters
* - L-BPH_g.dat
- Helical Base-steps parameters
* - HelAxis_g.dat
- Local helical axis coordinates
* - MGroove_g.dat
- Major and Minor grooves
* - HelixRad_g.dat
- Local helical radius
* - BackBoneCHiDihedrals_g.dat
- Backbone dihedral angles including Chi-dihedral
* - SugarDihedrals_g.dat
- Sugar dihedral angles including puckering type
* - Stretch_g.xvg
- Stretch of base-pairs as a function of time
* - Shear_g.xvg
- Shear of base-pairs as a function of time
* - Stagger_g.xvg
- Stagger of base-pairs as a function of time
* - Buckle_g.xvg
- Buckle of base-pairs as a function of time
* - Propeller_g.xvg
- Propeller of base-pairs as a function of time
* - Opening_g.xvg
- Opening of base-pairs as a function of time
* - Shift_g.xvg
- Shift of base-steps as a function of time
* - Slide_g.xvg
- Slide of base-steps as a function of time
* - Rise_g.xvg
- Rise of base-steps as a function of time
* - Tilt_g.xvg
- Tilt of base-steps as a function of time
* - Roll_g.xvg
- Roll of base-steps as a function of time
* - Twist_g.xvg
- Twist of base-steps as a function of time
* - X-displacement_g.xvg
- Helical X-displacement of helical base-steps as a function of time
* - Y-displacement_g.xvg
- Helical Y-displacement of base-steps as a function of time
* - Tip_g.xvg
- Tip of base-steps as a function of time
* - Inclination_g.xvg
- Helical inclination of base-steps as a function of time
* - H-twist_g.xvg
- Helical twist of helical base-steps as a function of time
* - H-rise_g.xvg
- Helical rise of base-steps as a function of time
* - Avg_Local_BP_param_g.xvg
- Average and standard deviations of Base-pairs parameters with respect to base-pairs
* - Avg_bp_step_param_g.xvg
- Average and standard deviations of Base-steps parameters with respect to base-steps
* - Avg_bp_helical_param_g.xvg
- Average and standard deviations of helical Base-steps parameters with respect to base-steps |
Name of these files could be change by setting different suffix instead of ``g`` using ``-name`` option. These
files could be used with the Python APIs or scripts for further analysis.