.. _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:``] [:strong:`-box` :emphasis:``] [:strong:`-angles` :emphasis:``] [:strong:`-d` :emphasis:``] [:strong:`-[no]c`] [:strong:`-center` :emphasis:``] [:strong:`-aligncenter` :emphasis:``] [:strong:`-align` :emphasis:``] [:strong:`-translate` :emphasis:``] [:strong:`-rotate` :emphasis:``] [:strong:`-[no]princ`] [:strong:`-scale` :emphasis:``] [:strong:`-density` :emphasis:``] [:strong:`-[no]pbc`] [:strong:`-resnr` :emphasis:``] [:strong:`-[no]grasp`] [:strong:`-rvdw` :emphasis:``] [:strong:`-[no]sig56`] [:strong:`-[no]vdwread`] [:strong:`-[no]atom`] [:strong:`-[no]legend`] [:strong:`-label` :emphasis:``] [:strong:`-[no]conect`] Description ----------- ``gmx editconf`` converts generic structure format to :ref:`.gro `, ``.g96`` or :ref:`.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 ` 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 ` 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 ` (.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 ` 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 `, :ref:`.xpm `, :ref:`.eps ` and :ref:`.pdb ` files ``-[no]ndef`` (no) Choose output from default index groups ``-bt`` (triclinic) Box type for ``-box`` and ``-d``: triclinic, cubic, dodecahedron, octahedron ``-box`` (0 0 0) Box vector lengths (a,b,c) ``-angles`` (90 90 90) Angles between the box vectors (bc,ac,ab) ``-d`` (0) Distance between the solute and the box ``-[no]c`` (no) Center molecule in box (implied by ``-box`` and ``-d``) ``-center`` (0 0 0) Shift the geometrical center to (x,y,z) ``-aligncenter`` (0 0 0) Center of rotation for alignment ``-align`` (0 0 0) Align to target vector ``-translate`` (0 0 0) Translation ``-rotate`` (0 0 0) Rotation around the X, Y and Z axes in degrees ``-[no]princ`` (no) Orient molecule(s) along their principal axes ``-scale`` (1 1 1) Scaling factor ``-density`` (1000) Density (g/L) of the output box achieved by scaling ``-[no]pbc`` (no) Remove the periodicity (make molecule whole again) ``-resnr`` (-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`` (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`` (A) Add chain label for all residues ``-[no]conect`` (no) Add CONECT records to a :ref:`.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 `. .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at .