Ubuntu Manpage: gmx-editconf - Convert and manipulates structure files

Provided by: gromacs-data_2021.4-2_all

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. The -center option can be used to shift the
geometric center of the system from the default of (x/2, y/2, z/2) implied by -c to some
other value.

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 the number of B-factors is larger than the number of the 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)
              Shift the geometrical center to (x,y,z)

       -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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