Provided by: gromacs-data_4.5.5-1_all bug

NAME

       editconf - edits the box and writes subgroups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       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  -sig56
       real -[no]vdwread -[no]atom -[no]legend -label string -[no]conect

DESCRIPTION

        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
       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  .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  .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.

FILES

       -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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        Set the nicelevel

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]ndefno
        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

       -[no]cno
        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
        Translation

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

       -[no]princno
        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]pbcno
        Remove the periodicity (make molecule whole again)

       -resnr int -1
         Renumber residues starting from resnr

       -[no]graspno
        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 sigma/2

       -[no]vdwreadno
        Read  the  Van der Waals radii from the file vdwradii.dat rather than computing the radii
       based on the force field

       -[no]atomno
        Force B-factor attachment per atom

       -[no]legendno
        Make B-factor legend

       -label string A
        Add chain label for all residues

       -[no]conectno
        Add CONECT records to a  .pdb file when written. Can only be  done  when  a  topology  is
       present

KNOWN PROBLEMS

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

SEE ALSO

       gromacs(7)

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

                                          Mon 4 Apr 2011                              editconf(1)