Ubuntu Manpage: editconf - edits the box and writes subgroups VERSION 4.6.5

Provided by: gromacs-data_4.6.5-1build1_all

NAME

       editconf - edits the box and writes subgroups VERSION 4.6.5

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 -[no]sig56 -[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

       -[no]sig56no
        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