editconf

| ## editconf Main Table of Contents | VERSION 4.5 Thu 26 Aug 2010

### 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. 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.

### Files

option | filename | type | description
--- | --- | --- | ---
`-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

option | type | default | description
--- | --- | --- | ---
`-[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

### Known problems

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

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