editconf VERSION 3.3_beta_20050823

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 -box and -d

will center the system in the box.

Option -bt determines the box type: tric is a triclinic box, cubic is a cubic box, dodecahedron is 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 tric the size of the system in the x, y and z directions is used. With -d and cubic ,

dodecahedron or octahedron the diameter of the system is used, which is the largest distance between two atoms.

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 can be scaled to give a certain density (option

-density ). 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 Generic structure: gro g96 pdb tpr tpb tpa xml

-n index.ndx Input, Opt. Index file

-o out.gro Output, Opt. Generic structure: gro g96 pdb xml

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

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

-[no]h no Print help info and quit

-nice int 0 Set the nicelevel

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

-[no]ndef no Choose output from default index groups

-bt enum tric Box type for -box and -d: tric , 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]c no Center molecule in box (implied by -box and -d)

-center vector 0 0 0 Coordinates of geometrical center

-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]vol yes Compute and print volume of the box

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

-[no]grasp no 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]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

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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.