editconf - edits the box and writes subgroups
editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf
bfact.dat -[no]h -nice int -[no]w -[no]ndef -bt enum -box vector
-angles vector -d real -[no]c -center vector -translate vector -rotate
vector -[no]princ -scale vector -density real -[no]vol -[no]pbc
-[no]grasp -rvdw real -sig56 real -[no]vdwread -[no]atom -[no]legend
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.
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. The volume of a
dodecahedron is 0.71 and that of a truncated octahedron is 0.77 of that
of a cubic box with the same periodic image distance.
Option -box requires only one value for a cubic box, dodecahedron and
a truncated octahedron.
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 can not 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, 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, when the factor -1
is given in one dimension, one obtains a mirror image, mirrored in one
of the plains, 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 sizes 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 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
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.
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:
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.
-f conf.gro Input
Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt.
-o out.gro Output, Opt.
Structure file: gro g96 pdb
-mead mead.pqr Output, Opt.
Coordinate file for MEAD
-bf bfact.dat Input, Opt.
Generic data file
Print help info and quit
-nice int 0
Set the nicelevel
View output xvg, xpm, eps and pdb files
Choose output from default index groups
-bt enum triclinic
Box type for -box and -d: triclinic, cubic, dodecahedron or
-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
Center molecule in box (implied by -box and -d)
-center vector 0 0 0
Coordinates of geometrical center
-translate vector 0 0 0
-rotate vector 0 0 0
Rotation around the X, Y and Z axes in degrees
Orient molecule(s) along their principal axes
-scale vector 1 1 1
-density real 1000
Density (g/l) of the output box achieved by scaling
Compute and print volume of the box
Remove the periodicity (make molecule whole again)
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
-sig56 real 0
Use rmin/2 (minimum in the Van der Waals potential) rather than
Read the Van der Waals radii from the file vdwradii.dat rather than
computing the radii based on the force field
Force B-factor attachment per atom
Make B-factor legend
-label string A
Add chain label for all residues
- For complex molecules, the periodicity removal routine may break
down, in that case you can use trjconv
More information about GROMACS is available at
Thu 16 Oct 2008 editconf(1)