do_x3dna for VMD

do_x3dna for VMD is written in Tcl language and it can be used as VMD plugin or Tcl package with VMD. It produces output files in same format as generated by GROMACS do_x3dna.

Note

do_x3dna VMD plugin does not depend on GROMACS do_x3dna. Therefore, do_x3dna for GROMACS is not necessary to run do_x3dna VMD plugin.

Following parameters are calculated using 3DNA package for each frame and written in separate files as a function of time.

• Base-pairs

• Hydrogen bonds between base-pairs

• Base-pairs parameters

• Base-steps parameters

• Helical Base-steps parameters

• 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 could be used with the dnaMD module and tools for further analysis.

Download

do_x3dna package can be downloaded by either of following two steps.

1. Use git:

git clone -b master --single-branch https://github.com/rjdkmr/do_x3dna

2. Download either zipball or tarball.

Installation

Follow these steps to install do_x3dna as VMD plugin.

cd do_x3dna
cd vmd
cp -r do_x3dna /usr/local/lib/vmd/plugins/noarch/tcl/.

If VMD is not at default location, copy vmd/do_x3dna in plugins/noarch/tcl/ vmd directory.

How to use?

To use do_x3dna VMD plugin, 3DNA package should be installed and $X3DNA environment variable (Detail is given in 3DNA manual) should be defined.

It can be either used from VMD TkConsole or through a Tcl scrip.

For example, below section can be used directly in VMD TkConsole or save it as a tcl script file.

package require do_x3dna

set trajectories {traj-1.dcd traj-2.dcd}
do_x3dna -tp example.psf -refFrame example.pdb -trajs $trajectories -dnaAtoms "nucleic" -fitAtoms "name P"

# Uncomment it when using as script
# quit

Above example can be run through a script.

vmd -dispdev text -e run_script.tcl

Note

We recommend to use do_x3dna plugin through script with VMD as shown above. -dispdev text execute VMD in text mode as command and does not open Display window.

Execute following command to get full help

package require do_x3dna
do_x3dna -help

Usage

Note

Before running do_x3dna, make sure 3DNA package is correctly working for the input DNA/RNA structure. To check it, run do_x3dna with only reference frame instead of trajectory file. -noisy option switch-on the output message from the 3DNA package on the display that would be necessary to troubleshoot problems related to the 3DNA package Most common problem is the residue names mismatch in input DNA/RNA structure and the 3DNA package dictionary.

Note

Only PBC corrected trajectory files should be used as inputs.

Note

If -fitAtoms is provided, this atoms group is used to superimpose current frame on reference frame. Most of the parameters are unaffected by this fitting, however coordinates of the local helical axis could mismatch with the input coordinates with the DNA/RNA.

Note

By default, bigdcd routine is used because it enables the trajectory reading frame by frame and allows to use very large trajectory. It can be switched-off by using -loadAll option.

Summary

do_x3dna -help -tp <file> -ftp <file type>
         -dnaAtoms <DNA atoms> -fitAtoms <Atoms to fit>
         -refFrame <Reference file> -refFrameType <reference file type>
         -trajs <List of trajectory files> -trajType <trajectory file type>
         -suffix <output suffix> -dt <time-step ps>
         -noisy -loadAll

OPTIONS

-help

Optional

Show help and exit.

-tp

Required

Topology-Parameter file with or without coordinates (psf/prmtop/pdb/gro). If it is pdb/gro containing coordinates of atoms, this will be used as reference frame for fitting and base-pair calculation. In case of coordinate files such as pdb/gro, -refFrame will be only considered as an additional frame as a part of trajectory.

-ftp

Optional

File format of Topology-Parameter file. If not provided, file format is automatically determined by VMD using extension.

-dnaAtoms

Optional

Atoms belonging to DNA/RNA. If not provided, by default "nucleic" is used to select atoms.

-fitAtoms

Optional

Atoms for fitting to reference frame. If not provided, fitting will be not done.

-refFrame

Required/Optional

Reference coordinate file for fitting and base-pair calculation. In case of psf and prmtop file, this is required because these files do not contain coordinates.

-refFrameType

Optional

File format of Reference frame file. If not provided, file format is automatically determined by VMD using extension.

-trajs

Optional

List of trajectory files. If not provided, only first frame will be used for calculation. It is useful to check whether 3DNA is working correctly with -noisy option.

-trajType

Optional

File format of trajectory file. If not provided, file format is automatically determined by VMD using extension.

-suffix

Optional

Suffix for all output file names. If not provided, "g" is used by default.

-dt

Optional

Time-step between frames in ps. It is dumped in output files and make easier for plotting. If not provided, by default, its value is 1 ps.

-noisy

Optional

Display messages and errors from 3DNA programs find_pair and analyze.

-loadAll

Optional

With this option, at first all trajectory will be loaded and then 3DNA will be executed for each frame. Therefore, large memory will be consumed for large trajectory.

Output Files

Following files are generated from do_x3dna:

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 dihederal angles including Chi-dihedral
SugarDihedrals_g.dat	Sugar dihedral angles including puckering type

Name of these files could be change by setting different suffix instead of g using -suffix option. These files could be used with the dnaMD module and tools for further analysis.