gmx-editconf(1) GROMACS Manual gmx-editconf(1)NAMEgmx-editconf - Convert and manipulates structure files
SYNOPSIS
gmx editconf [-f [<.gro/.g96/...>]] [-n [<.ndx>]]
[-o [<.gro/.g96/...>]] [-mead [<.pqr>]] [-bf [<.dat>]]
[-nice <int>] [-[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.
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 sig‐
nificantly 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 peri‐
odicity 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 fol‐
lowed by a B-factor. The B-factors will be attached per residue unless
an index is larger than the number of 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 electro‐
statics program (Poisson-Boltzmann solver) can be made. A further pre‐
requisite 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 and output files:
-f [<.gro/.g96/...>] (conf.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.gro/.g96/...>] (out.gro) (Output, Optional)
Structure file: gro g96 pdb brk ent esp
-mead [<.pqr>] (mead.pqr) (Output, Optional)
Coordinate file for MEAD
-bf [<.dat>] (bfact.dat) (Input, Optional)
Generic data file
Other options:
-nice <int> (0)
Set the nicelevel
-[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, octahe‐
dron
-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)
Coordinates of geometrical center
-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 is present
KNOWN ISSUES
- For complex molecules, the periodicity removal routine may break
down, in that case you can use gmx trjconv.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-editconf(1)
