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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  be-
       tween  two  opposite hexagons.  Relative	to a cubic box with some peri-
       odic image distance, the	volume of a dodecahedron with this same	 peri-
       odic  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 peri-
       odicity 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 fol-
       lowed 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	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, ef-
       fectively making	a legend for viewing.

       With  the option	-mead a	special	.pdb (.pqr) file for the MEAD electro-
       statics program (Poisson-Boltzmann solver) can be made. A further  pre-
       requisite  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/^a|>] (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/^a|>] (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,	 octa-
	      hedron

       -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 ra-
	      dius 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 is present

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

       o in that case you can use gmx trjconv.

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020		       GMX-EDITCONF(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT

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