editconf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       editconf(1)

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 vec-
       tor -angles vector -d real -[no]c -center vector -aligncenter vector -align vector -translate vector -rotate vector -[no]princ -scale  vec-
       tor -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 repre-
       sents 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, effec-
       tively 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)