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. 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 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 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 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, 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.
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.
|-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|
|-[no]h||gmx_bool||no||Print help info and quit|
|-[no]version||gmx_bool||no||Print version info and quit|
|-nice||int||0||Set the nicelevel|
|-[no]w||gmx_bool||no||View output xvg, xpm, eps and pdb files|
|-[no]ndef||gmx_bool||no||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]c||gmx_bool||no||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]princ||gmx_bool||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||gmx_bool||no||Remove the periodicity (make molecule whole again)|
|-[no]grasp||gmx_bool||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||gmx_bool||no||Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field|
|-[no]atom||gmx_bool||no||Force B-factor attachment per atom|
|-[no]legend||gmx_bool||no||Make B-factor legend|
|-label||string||A||Add chain label for all residues|
|-[no]conect||gmx_bool||no||Add CONECT records to a pdb file when written. Can only be done when a topology is present|