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.

  • 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 of output files from do_x3dna
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.