This is the command gmx-editconf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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:
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)
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.
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