--- name: "editconf" section: "1" platform: "linux" package: "gromacs-data" version: "5.0.2-1" release: "Debian 8 (Jessie)" platforms: ["linux"] url: "https://new.carta.tech/gmx-editconf" --- # editconf(1) Convert and manipulates structure files Part of [gmx-editconf(1)](/gmx-editconf/1.md). ## NAME gmx-editconf - Convert and manipulates structure files ## SYNOPSIS gmx editconf \[-f \[\<.gro/.g96/...\>\]\] \[-n \[\<.ndx\>\]\]\ \[-o \[\<.gro/.g96/...\>\]\] \[-mead \[\<.pqr\>\]\] \[-bf \[\<.dat\>\]\]\ \[-nice \\] \[-\[no\]w\] \[-\[no\]ndef\] \[-bt \\]\ \[-box \\] \[-angles \\] \[-d \\] \[-\[no\]c\]\ \[-center \\] \[-aligncenter \\]\ \[-align \\] \[-translate \\]\ \[-rotate \\] \[-\[no\]princ\] \[-scale \\]\ \[-density \\] \[-\[no\]pbc\] \[-resnr \\] \[-\[no\]grasp\]\ \[-rvdw \\] \[-\[no\]sig56\] \[-\[no\]vdwread\] \[-\[no\]atom\]\ \[-\[no\]legend\] \[-label \\] \[-\[no\]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. 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: **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)](/sqrt/3.md)/2. ## OPTIONS Options to specify input and output files: **-f** *\[\<.gro/.g96/...\>\] (conf.gro) (Input)*\ Structure file: gro g96 pdb brk ent esp tpr tpb tpa **-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\ Index file **-o** *\[\<.gro/.g96/...\>\] (out.gro) (Output, Optional)*\ Structure file: gro g96 pdb brk ent esp **-mead** *\[\<.pqr\>\] (mead.pqr) (Output, Optional)*\ Coordinate file for MEAD **-bf** *\[\<.dat\>\] (bfact.dat) (Input, Optional)*\ Generic data file Other options: **-nice** *\ (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** *\ (triclinic)*\ Box type for **-box** and **-d**: triclinic, cubic, dodecahedron, octahedron **-box** *\ (0 0 0)*\ Box vector lengths (a,b,c) **-angles** *\ (90 90 90)*\ Angles between the box vectors (bc,ac,ab) **-d** *\ (0)*\ Distance between the solute and the box **-\[no\]c** *(no)*\ Center molecule in box (implied by **-box** and **-d**) **-center** *\ (0 0 0)*\ Coordinates of geometrical center **-aligncenter** *\ (0 0 0)*\ Center of rotation for alignment **-align** *\ (0 0 0)*\ Align to target vector **-translate** *\ (0 0 0)*\ Translation **-rotate** *\ (0 0 0)*\ Rotation around the X, Y and Z axes in degrees **-\[no\]princ** *(no)*\ Orient molecule(s) along their principal axes **-scale** *\ (1 1 1)*\ Scaling factor **-density** *\ (1000)*\ Density (g/L) of the output box achieved by scaling **-\[no\]pbc** *(no)*\ Remove the periodicity (make molecule whole again) **-resnr** *\ (-1)*\ Renumber residues starting from resnr **-\[no\]grasp** *(no)*\ Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field **-rvdw** *\ (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** *\ (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 \- For complex molecules, the periodicity removal routine may break down, in that case you can use **gmx trjconv**. ## SEE ALSO **[gromacs(7)](/gromacs/7.md)** More information about **GROMACS** is available at \<*http://www.gromacs.org/*\>.