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GMX-EDITCONF(1) 		     GROMACS			 GMX-EDITCONF(1)

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-di-
     rections  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  de-
     crease  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 ob-
     tained.

     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-fac-
     tors  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 op-
     tion 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 electrostat-
     ics 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 (tpr file) is present

KNOWN ISSUES
     * For complex molecules, the periodicity removal routine may break down,

     * in that case you can use gmx trjconv.

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			 GMX-EDITCONF(1)
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