.. _gmx editconf:
gmx editconf
============
Synopsis
--------
.. parsed-literal::
gmx editconf [:strong:`-f` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-bf` :emphasis:`[<.dat>]`]
[:strong:`-o` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-mead` :emphasis:`[<.pqr>]`] [:strong:`-[no]w`]
[:strong:`-[no]ndef`] [:strong:`-bt` :emphasis:`<enum>`] [:strong:`-box` :emphasis:`<vector>`]
[:strong:`-angles` :emphasis:`<vector>`] [:strong:`-d` :emphasis:`<real>`] [:strong:`-[no]c`]
[:strong:`-center` :emphasis:`<vector>`] [:strong:`-aligncenter` :emphasis:`<vector>`]
[:strong:`-align` :emphasis:`<vector>`] [:strong:`-translate` :emphasis:`<vector>`]
[:strong:`-rotate` :emphasis:`<vector>`] [:strong:`-[no]princ`] [:strong:`-scale` :emphasis:`<vector>`]
[:strong:`-density` :emphasis:`<real>`] [:strong:`-[no]pbc`] [:strong:`-resnr` :emphasis:`<int>`] [:strong:`-[no]grasp`]
[:strong:`-rvdw` :emphasis:`<real>`] [:strong:`-[no]sig56`] [:strong:`-[no]vdwread`] [:strong:`-[no]atom`]
[:strong:`-[no]legend`] [:strong:`-label` :emphasis:`<string>`] [:strong:`-[no]conect`]
Description
-----------
``gmx editconf`` converts generic structure format to :ref:`.gro <gro>`, ``.g96``
or :ref:`.pdb <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 :ref:`.gro <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 :ref:`.pdb <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 :ref:`.pdb <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 :ref:`.pdb <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: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`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: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp
``-mead`` [<.pqr>] (mead.pqr) (Optional)
Coordinate file for MEAD
Other options:
``-[no]w`` (no)
View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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 :ref:`.pdb <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 :doc:`gmx trjconv <gmx-trjconv>`.
.. only:: man
See also
--------
:manpage:`gmx(1)`
More information about |Gromacs| is available at <http://www.gromacs.org/>.