.TH gmx-editconf 1 "" "VERSION 5.0.2" "GROMACS Manual" .SH NAME gmx-editconf \- Convert and manipulates structure files .SH 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] .SH DESCRIPTION \fBgmx editconf\fR converts generic structure format to \fB.gro\fR, \fB.g96\fR or \fB.pdb\fR. The box can be modified with options \fB\-box\fR, \fB\-d\fR and \fB\-angles\fR. Both \fB\-box\fR and \fB\-d\fR will center the system in the box, unless \fB\-noc\fR is used. Option \fB\-bt\fR determines the box type: \fBtriclinic\fR is a triclinic box, \fBcubic\fR is a rectangular box with all sides equal \fBdodecahedron\fR represents a rhombic dodecahedron and \fBoctahedron\fR 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 \fB\-box\fR requires only one value for a cubic, rhombic dodecahedral, or truncated octahedral box. With \fB\-d\fR and a \fBtriclinic\fR box the size of the system in the \fIx\fR\-, \fIy\fR\-, and \fIz\fR\-directions is used. With \fB\-d\fR and \fBcubic\fR, \fBdodecahedron\fR or \fBoctahedron\fR boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance. Option \fB\-angles\fR is only meaningful with option \fB\-box\fR and a triclinic box and cannot be used with option \fB\-d\fR. When \fB\-n\fR or \fB\-ndef\fR is set, a group can be selected for calculating the size and the geometric center, otherwise the whole system is used. \fB\-rotate\fR rotates the coordinates and velocities. \fB\-princ\fR aligns the principal axes of the system along the coordinate axes, with the longest axis aligned with the \fIx\fR\-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 \fB\-density\fR). Note that this may be inaccurate in case a \fB.gro\fR 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 \fB.pdb\fR files, B\-factors can be added with the \fB\-bf\fR 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 \fB\-atom\fR option is set. Obviously, any type of numeric data can be added instead of B\-factors. \fB\-legend\fR 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 \fB\-mead\fR a special \fB.pdb\fR (\fB.pqr\fR) 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 \fB\-grasp\fR is similar, but it puts the charges in the B\-factor and the radius in the occupancy. Option \fB\-align\fR allows alignment of the principal axis of a specified group against the given vector, with an optional center of rotation specified by \fB\-aligncenter\fR. Finally, with option \fB\-label\fR, \fBeditconf\fR can add a chain identifier to a \fB.pdb\fR 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: \fBgmx editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out\fR where \fBveclen\fR is the size of the cubic box times sqrt(3)/2. .SH OPTIONS Options to specify input and output files: .BI "\-f" " [<.gro/.g96/...>] (conf.gro) (Input)" Structure file: gro g96 pdb brk ent esp tpr tpb tpa .BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)" Index file .BI "\-o" " [<.gro/.g96/...>] (out.gro) (Output, Optional)" Structure file: gro g96 pdb brk ent esp .BI "\-mead" " [<.pqr>] (mead.pqr) (Output, Optional)" Coordinate file for MEAD .BI "\-bf" " [<.dat>] (bfact.dat) (Input, Optional)" Generic data file Other options: .BI "\-nice" " (0)" Set the nicelevel .BI "\-[no]w" " (no)" View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files .BI "\-[no]ndef" " (no)" Choose output from default index groups .BI "\-bt" " (triclinic)" Box type for \fB\-box\fR and \fB\-d\fR: triclinic, cubic, dodecahedron, octahedron .BI "\-box" " (0 0 0)" Box vector lengths (a,b,c) .BI "\-angles" " (90 90 90)" Angles between the box vectors (bc,ac,ab) .BI "\-d" " (0)" Distance between the solute and the box .BI "\-[no]c" " (no)" Center molecule in box (implied by \fB\-box\fR and \fB\-d\fR) .BI "\-center" " (0 0 0)" Coordinates of geometrical center .BI "\-aligncenter" " (0 0 0)" Center of rotation for alignment .BI "\-align" " (0 0 0)" Align to target vector .BI "\-translate" " (0 0 0)" Translation .BI "\-rotate" " (0 0 0)" Rotation around the X, Y and Z axes in degrees .BI "\-[no]princ" " (no)" Orient molecule(s) along their principal axes .BI "\-scale" " (1 1 1)" Scaling factor .BI "\-density" " (1000)" Density (g/L) of the output box achieved by scaling .BI "\-[no]pbc" " (no)" Remove the periodicity (make molecule whole again) .BI "\-resnr" " (-1)" Renumber residues starting from resnr .BI "\-[no]grasp" " (no)" Store the charge of the atom in the B\-factor field and the radius of the atom in the occupancy field .BI "\-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 .BI "\-[no]sig56" " (no)" Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 .BI "\-[no]vdwread" " (no)" Read the Van der Waals radii from the file \fBvdwradii.dat\fR rather than computing the radii based on the force field .BI "\-[no]atom" " (no)" Force B\-factor attachment per atom .BI "\-[no]legend" " (no)" Make B\-factor legend .BI "\-label" " (A)" Add chain label for all residues .BI "\-[no]conect" " (no)" Add CONECT records to a \fB.pdb\fR file when written. Can only be done when a topology is present .SH KNOWN ISSUES \- For complex molecules, the periodicity removal routine may break down, in that case you can use \fBgmx trjconv\fR. .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.