--- name: "gmx-editconf" section: "1" platform: "linux" package: "gromacs-data" version: "2025.2-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/gmx-editconf" --- # gmx-editconf(1) Convert and manipulates structure files ## NAME gmx-editconf - Convert and manipulates structure files ## SYNOPSIS ``` gmx editconf [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-bf [<.dat>]] [-o [<.gro/.g96/...>]] [-mead [<.pqr>]] [-[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. The **-center** option can be used to shift the geometric center of the system from the default of (x/2, y/2, z/2) implied by **-c** to some other value. 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 the number of B-factors is larger than the number of the 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 files: - **-f \[\<.gro/.g96/...\>\] (conf.gro)** Structure file: *gro* *g96* *pdb* brk ent esp *tpr* - **-n \[\<.ndx\>\] (index.ndx) (Optional)** Index file - **-bf \[\<.dat\>\] (bfact.dat) (Optional)** Generic data file Options to specify output files: - **-o \[\<.gro/.g96/...\>\] (out.gro) (Optional)** Structure file: *gro* *g96* *pdb* brk ent esp - **-mead \[\<.pqr\>\] (mead.pqr) (Optional)** Coordinate file for MEAD Other options: - **-\[no\]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)** Shift the geometrical center to (x,y,z) - **-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 (tpr file) is present ## KNOWN ISSUES - • For complex molecules, the periodicity removal routine may break down, - • in that case you can use *gmx trjconv*. ## SEE ALSO **[gmx(1)](/gmx/1.md)** More information about GROMACS is available at \<*http://www.gromacs.org/*\>. ## COPYRIGHT 2025, GROMACS development team