Man page - gmx-editconf(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
- gmx-genrestr(1)
- gmx-bar(1)
- gmx-lie(1)
- gmx-filter(1)
- gmx-scattering(1)
- gmx-anaeig(1)
- gmx-covar(1)
- gmx_d(1)
- gmx-genconf(1)
- gmx-mdrun(1)
- gmx-velacc(1)
- gmx-tcaf(1)
- gmx-insert-molecules(1)
- gmx-bundle(1)
- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
- gmx-confrms(1)
- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
- gmx-current(1)
- gmx-freevolume(1)
- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
- gmx-gyrate(1)
- gmx-solvate(1)
- gmx-densmap(1)
- gmx-rotacf(1)
- gmx-helix(1)
- gmx_mpi(1)
- gmx-convert-tpr(1)
- gmx-convert-trj(1)
- gmx-polystat(1)
- gmx-angle(1)
- gmx-xpm2ps(1)
- gmx-pdb2gmx(1)
- gmx-sasa(1)
- gmx-x2top(1)
- gmx-trjcat(1)
- gmx-h2order(1)
- gmx-nmr(1)
- gmx-dump(1)
- gmx-spol(1)
- gmx-distance(1)
- gmx-clustsize(1)
- gmx-rama(1)
- gmx-chi(1)
- gmx-pme_error(1)
- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
- gmx-tune_pme(1)
- gmx-grompp(1)
- gmx-make_edi(1)
- gmx-trajectory(1)
- gmx-dipoles(1)
- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
- gmx-analyze(1)
- demux(1)
- gmx-disre(1)
- gmx-saxs-legacy(1)
- gmx-sigeps(1)
- gmx-mdmat(1)
- xplor2gmx(1)
- gmx-check(1)
- gmx-vanhove(1)
- gmx-dssp(1)
- gmx-densorder(1)
- gmx-principal(1)
- gmx-mindist(1)
- gmx-spatial(1)
- gmx-wham(1)
- gmx-rmsf(1)
- gmx-dos(1)
- gmx-mk_angndx(1)
- gmx-nmens(1)
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- gmx-sorient(1)
- gmx-help(1)
- gmx-hbond-legacy(1)
- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-EDITCONF
NAMESYNOPSIS
DESCRIPTION
OPTIONS
KNOWN ISSUES
SEE ALSO
COPYRIGHT
NAME
gmx-editconf - Convert and manipulates structure files
SYNOPSIS
gmx editconf
[
-f
[<.gro/.g96/...>]
] [
-n
[<.ndx>]
] [
-bf
[<.dat>]
]
[
-o
[<.gro/.g96/...>]
] [
-mead
[<.pqr>]
] [
-[no]w
]
[
-[no]ndef
] [
-bt
<enum>
]
[
-box
<vector>
]
[
-angles
<vector>
] [
-d
<real>
] [
-[no]c
]
[
-center
<vector>
] [
-aligncenter
<vector>
]
[
-align
<vector>
] [
-translate
<vector>
]
[
-rotate
<vector>
] [
-[no]princ
]
[
-scale
<vector>
]
[
-density
<real>
] [
-[no]pbc
]
[
-resnr
<int>
] [
-[no]grasp
]
[
-rvdw
<real>
] [
-[no]sig56
]
[
-[no]vdwread
] [
-[no]atom
]
[
-[no]legend
] [
-label
<string>
]
[
-[no]conect
]
DESCRIPTION
gmx editconf converts generic structure format to .gro , .g96 or .pdb .
The box can be modified with options -box , -d and -angles . Both -box and -d will center the system in the box, unless -noc is used. The -center option can be used to shift the geometric center of the system from the default of (x/2, y/2, z/2) implied by -c to some other value.
Option -bt determines the box type: triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times.
Option -box requires only one value for a cubic, rhombic dodecahedral, or truncated octahedral box.
With -d and a triclinic box the size of the system in the x -, y -, and z -directions is used. With -d and cubic , dodecahedron or octahedron boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance.
Option -angles is only meaningful with option -box and a triclinic box and cannot be used with option -d .
When -n or -ndef is set, a group can be selected for calculating the size and the geometric center, otherwise the whole system is used.
-rotate rotates the coordinates and velocities.
-princ aligns the principal axes of the system along the coordinate axes, with the longest axis aligned with the x -axis. This may allow you to decrease the box volume, but beware that molecules can rotate significantly in a nanosecond.
Scaling is applied before any of the other operations are performed. Boxes and coordinates can be scaled to give a certain density (option -density ). Note that this may be inaccurate in case a .gro file is given as input. A special feature of the scaling option is that when the factor -1 is given in one dimension, one obtains a mirror image, mirrored in one of the planes. When one uses -1 in three dimensions, a point-mirror image is obtained.
Groups are selected after all operations have been applied.
Periodicity can be removed in a crude manner. It is important that the box vectors at the bottom of your input file are correct when the periodicity is to be removed.
When writing .pdb files, B-factors can be added with the -bf option. B-factors are read from a file with with following format: first line states number of entries in the file, next lines state an index followed by a B-factor. The B-factors will be attached per residue unless the number of B-factors is larger than the number of the residues or unless the -atom option is set. Obviously, any type of numeric data can be added instead of B-factors. -legend will produce a row of CA atoms with B-factors ranging from the minimum to the maximum value found, effectively making a legend for viewing.
With the option -mead a special .pdb (.pqr) file for the MEAD electrostatics program (Poisson-Boltzmann solver) can be made. A further prerequisite is that the input file is a run input file. The B-factor field is then filled with the Van der Waals radius of the atoms while the occupancy field will hold the charge.
The option -grasp is similar, but it puts the charges in the B-factor and the radius in the occupancy.
Option -align allows alignment of the principal axis of a specified group against the given vector, with an optional center of rotation specified by -aligncenter .
Finally, with option -label , editconf can add a chain identifier to a .pdb file, which can be useful for analysis with e.g. Rasmol.
To convert a truncated octrahedron file produced by a package which uses a cubic box with the corners cut off (such as GROMOS), use:
gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
where veclen is the size of the cubic box times sqrt(3)/2.
OPTIONS
Options to
specify input files:
-f [<.gro/.g96/...>] (conf.gro)
Structure file: gro g96 pdb brk ent esp tpr
-n [<.ndx>] (index.ndx) (Optional)
Index file
-bf [<.dat>] (bfact.dat) (Optional)
Generic data file
Options to
specify output files:
-o [<.gro/.g96/...>] (out.gro) (Optional)
Structure file: gro g96 pdb brk ent esp
-mead [<.pqr>] (mead.pqr) (Optional)
Coordinate file for MEAD
Other options:
-[no]w (no)
View output .xvg , .xpm , .eps and .pdb files
-[no]ndef (no)
Choose output from default index groups
-bt <enum> (triclinic)
Box type for -box and -d : triclinic, cubic, dodecahedron, octahedron
-box <vector> (0 0 0)
Box vector lengths (a,b,c)
-angles <vector> (90 90 90)
Angles between the box vectors (bc,ac,ab)
-d <real> (0)
Distance between the solute and the box
-[no]c (no)
Center molecule in box (implied by -box and -d )
-center <vector> (0 0 0)
Shift the geometrical center to (x,y,z)
-aligncenter <vector> (0 0 0)
Center of rotation for alignment
-align <vector> (0 0 0)
Align to target vector
-translate <vector> (0 0 0)
Translation
-rotate <vector> (0 0 0)
Rotation around the X, Y and Z axes in degrees
-[no]princ (no)
Orient molecule(s) along their principal axes
-scale <vector> (1 1 1)
Scaling factor
-density <real> (1000)
Density (g/L) of the output box achieved by scaling
-[no]pbc (no)
Remove the periodicity (make molecule whole again)
-resnr <int> (-1)
Renumber residues starting from resnr
-[no]grasp (no)
Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
-rvdw <real> (0.12)
Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
-[no]sig56 (no)
Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-[no]vdwread (no)
Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-[no]atom (no)
Force B-factor attachment per atom
-[no]legend (no)
Make B-factor legend
-label <string> (A)
Add chain label for all residues
-[no]conect (no)
Add CONECT records to a .pdb file when written. Can only be done when a topology (tpr file) is present
KNOWN ISSUES
|
• |
For complex molecules, the periodicity removal routine may break down, |
||
|
• |
in that case you can use gmx trjconv . |
SEE ALSO
gmx(1)
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2025, GROMACS development team