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
andchi
)sugar dihedral angles (
v0
,v1
,v2
,v3
andv4
)
These files are listed below.
Output Files
Following files are generated from do_x3dna
with and without options:
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.