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 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 -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 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 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.
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/>.
