editconf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c editconf(1)
NAME
editconf - edits the box and writes subgroups
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf bfact.dat -[no]h -[no]version -nice int -[no]w -[no]ndef -bt enum -box vec-
tor -angles vector -d real -[no]c -center vector -aligncenter vector -align vector -translate vector -rotate vector -[no]princ -scale vec-
tor -density real -[no]pbc -resnr int -[no]grasp -rvdw real -sig56 real -[no]vdwread -[no]atom -[no]legend -label string -[no]conect
DESCRIPTION
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 repre-
sents 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 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, effec-
tively 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:
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.
FILES
-f conf.gro Input
Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt.
Index file
-o out.gro Output, Opt.
Structure file: gro g96 pdb etc.
-mead mead.pqr Output, Opt.
Coordinate file for MEAD
-bf bfact.dat Input, Opt.
Generic data file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-[no]ndefno
Choose output from default index groups
-bt enum triclinic
Box type for -box and -d: triclinic, cubic, dodecahedron or 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]cno
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]princno
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]pbcno
Remove the periodicity (make molecule whole again)
-resnr int -1
Renumber residues starting from resnr
-[no]graspno
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 sigma/2
-[no]vdwreadno
Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-[no]atomno
Force B-factor attachment per atom
-[no]legendno
Make B-factor legend
-label string A
Add chain label for all residues
-[no]conectno
Add CONECT records to a .pdb file when written. Can only be done when a topology is present
KNOWN PROBLEMS
- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv.
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 editconf(1)