Provided by: gromacs-data_4.6.5-1build1_all bug


       editconf - edits the box and writes subgroups VERSION 4.6.5


       editconf  -f  conf.gro  -n  index.ndx  -o  out.gro  -mead  mead.pqr  -bf  bfact.dat -[no]h
       -[no]version -nice int -[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


        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

       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

       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:

        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.


       -f conf.gro Input
        Structure file: gro g96 pdb tpr etc.

       -n index.ndx Input, Opt.
        Index file

       -o out.gro Output, Opt.
        Structure file: gro g96 pdb etc.

       -mead mead.pqr Output, Opt.
        Coordinate file for MEAD

       -bf bfact.dat Input, Opt.
        Generic data file


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

        View output  .xvg,  .xpm,  .eps and  .pdb files

        Choose output from default index groups

       -bt enum triclinic
        Box type for  -box and  -d:  triclinic,  cubic,  dodecahedron or  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

        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

       -rotate vector 0 0 0
        Rotation around the X, Y and Z axes in degrees

        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

        Remove the periodicity (make molecule whole again)

       -resnr int -1
         Renumber residues starting from resnr

        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

        Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2

        Read  the Van der Waals radii from the file  vdwradii.dat rather than computing the radii
       based on the force field

        Force B-factor attachment per atom

        Make B-factor legend

       -label string A
        Add chain label for all residues

        Add CONECT records to a  .pdb file when written. Can only be  done  when  a  topology  is


       -  For complex molecules, the periodicity removal routine may break down, in that case you
       can use  trjconv.



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              editconf(1)