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       editconf - edits the box and writes subgroups

       VERSION 4.0.1


       editconf  -f  conf.gro  -n  index.ndx  -o  out.gro  -mead  mead.pqr -bf
       bfact.dat -[no]h -nice  int  -[no]w  -[no]ndef  -bt  enum  -box  vector
       -angles  vector -d real -[no]c -center vector -translate vector -rotate
       vector  -[no]princ  -scale  vector  -density  real  -[no]vol   -[no]pbc
       -[no]grasp  -rvdw  real  -sig56 real -[no]vdwread -[no]atom -[no]legend
       -label string


       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.

       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.   The  volume  of  a
       dodecahedron is 0.71 and that of a truncated octahedron is 0.77 of that
       of a cubic box with the same periodic image distance.

       Option  -box requires only one value for a cubic box, dodecahedron  and
       a truncated octahedron.

       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 can not 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,  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, when the factor -1
       is given in one dimension, one obtains a mirror image, mirrored in  one
       of  the  plains,  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  sizes  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.

       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 tpb tpa

       -n index.ndx Input, Opt.
        Index file

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

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

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


        Print help 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

       -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

       -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

        Compute and print volume of the box

        Remove the periodicity (make molecule whole again)

        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

       -sig56 real 0
        Use rmin/2 (minimum in  the  Van  der  Waals  potential)  rather  than

        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


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



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                    editconf(1)