.\" Man page generated from reStructuredText. . . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .TH "GMX-EDITCONF" "1" "Feb 28, 2024" "2024.1" "GROMACS" .SH NAME gmx-editconf \- Convert and manipulates structure files .SH SYNOPSIS .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C gmx editconf [\fB\-f\fP \fI[<.gro/.g96/...>]\fP] [\fB\-n\fP \fI[<.ndx>]\fP] [\fB\-bf\fP \fI[<.dat>]\fP] [\fB\-o\fP \fI[<.gro/.g96/...>]\fP] [\fB\-mead\fP \fI[<.pqr>]\fP] [\fB\-[no]w\fP] [\fB\-[no]ndef\fP] [\fB\-bt\fP \fI\fP] [\fB\-box\fP \fI\fP] [\fB\-angles\fP \fI\fP] [\fB\-d\fP \fI\fP] [\fB\-[no]c\fP] [\fB\-center\fP \fI\fP] [\fB\-aligncenter\fP \fI\fP] [\fB\-align\fP \fI\fP] [\fB\-translate\fP \fI\fP] [\fB\-rotate\fP \fI\fP] [\fB\-[no]princ\fP] [\fB\-scale\fP \fI\fP] [\fB\-density\fP \fI\fP] [\fB\-[no]pbc\fP] [\fB\-resnr\fP \fI\fP] [\fB\-[no]grasp\fP] [\fB\-rvdw\fP \fI\fP] [\fB\-[no]sig56\fP] [\fB\-[no]vdwread\fP] [\fB\-[no]atom\fP] [\fB\-[no]legend\fP] [\fB\-label\fP \fI\fP] [\fB\-[no]conect\fP] .ft P .fi .UNINDENT .UNINDENT .SH DESCRIPTION .sp \fBgmx editconf\fP converts generic structure format to \fI\%\&.gro\fP, \fB\&.g96\fP or \fI\%\&.pdb\fP\&. .sp The box can be modified with options \fB\-box\fP, \fB\-d\fP and \fB\-angles\fP\&. Both \fB\-box\fP and \fB\-d\fP will center the system in the box, unless \fB\-noc\fP is used. The \fB\-center\fP option can be used to shift the geometric center of the system from the default of (x/2, y/2, z/2) implied by \fB\-c\fP to some other value. .sp Option \fB\-bt\fP determines the box type: \fBtriclinic\fP is a triclinic box, \fBcubic\fP is a rectangular box with all sides equal \fBdodecahedron\fP represents a rhombic dodecahedron and \fBoctahedron\fP 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. .sp Option \fB\-box\fP requires only one value for a cubic, rhombic dodecahedral, or truncated octahedral box. .sp With \fB\-d\fP and a \fBtriclinic\fP box the size of the system in the \fIx\fP\-, \fIy\fP\-, and \fIz\fP\-directions is used. With \fB\-d\fP and \fBcubic\fP, \fBdodecahedron\fP or \fBoctahedron\fP boxes, the dimensions are set to the diameter of the system (largest distance between atoms) plus twice the specified distance. .sp Option \fB\-angles\fP is only meaningful with option \fB\-box\fP and a triclinic box and cannot be used with option \fB\-d\fP\&. .sp When \fB\-n\fP or \fB\-ndef\fP is set, a group can be selected for calculating the size and the geometric center, otherwise the whole system is used. .sp \fB\-rotate\fP rotates the coordinates and velocities. .sp \fB\-princ\fP aligns the principal axes of the system along the coordinate axes, with the longest axis aligned with the \fIx\fP\-axis. This may allow you to decrease the box volume, but beware that molecules can rotate significantly in a nanosecond. .sp 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\fP). Note that this may be inaccurate in case a \fI\%\&.gro\fP 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. .sp Groups are selected after all operations have been applied. .sp 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. .sp When writing \fI\%\&.pdb\fP files, B\-factors can be added with the \fB\-bf\fP 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 \fB\-atom\fP option is set. Obviously, any type of numeric data can be added instead of B\-factors. \fB\-legend\fP 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. .sp With the option \fB\-mead\fP a special \fI\%\&.pdb\fP (.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. .sp The option \fB\-grasp\fP is similar, but it puts the charges in the B\-factor and the radius in the occupancy. .sp Option \fB\-align\fP allows alignment of the principal axis of a specified group against the given vector, with an optional center of rotation specified by \fB\-aligncenter\fP\&. .sp Finally, with option \fB\-label\fP, \fBeditconf\fP can add a chain identifier to a \fI\%\&.pdb\fP file, which can be useful for analysis with e.g. Rasmol. .sp To convert a truncated octrahedron file produced by a package which uses a cubic box with the corners cut off (such as GROMOS), use: .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C gmx editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out .ft P .fi .UNINDENT .UNINDENT .sp where \fBveclen\fP is the size of the cubic box times sqrt(3)/2. .SH OPTIONS .sp Options to specify input files: .INDENT 0.0 .TP .B \fB\-f\fP [<.gro/.g96/...>] (conf.gro) Structure file: \fI\%gro\fP \fI\%g96\fP \fI\%pdb\fP brk ent esp \fI\%tpr\fP .TP .B \fB\-n\fP [<.ndx>] (index.ndx) (Optional) Index file .TP .B \fB\-bf\fP [<.dat>] (bfact.dat) (Optional) Generic data file .UNINDENT .sp Options to specify output files: .INDENT 0.0 .TP .B \fB\-o\fP [<.gro/.g96/...>] (out.gro) (Optional) Structure file: \fI\%gro\fP \fI\%g96\fP \fI\%pdb\fP brk ent esp .TP .B \fB\-mead\fP [<.pqr>] (mead.pqr) (Optional) Coordinate file for MEAD .UNINDENT .sp Other options: .INDENT 0.0 .TP .B \fB\-[no]w\fP (no) View output \fI\%\&.xvg\fP, \fI\%\&.xpm\fP, \fI\%\&.eps\fP and \fI\%\&.pdb\fP files .TP .B \fB\-[no]ndef\fP (no) Choose output from default index groups .TP .B \fB\-bt\fP (triclinic) Box type for \fB\-box\fP and \fB\-d\fP: triclinic, cubic, dodecahedron, octahedron .TP .B \fB\-box\fP (0 0 0) Box vector lengths (a,b,c) .TP .B \fB\-angles\fP (90 90 90) Angles between the box vectors (bc,ac,ab) .TP .B \fB\-d\fP (0) Distance between the solute and the box .TP .B \fB\-[no]c\fP (no) Center molecule in box (implied by \fB\-box\fP and \fB\-d\fP) .TP .B \fB\-center\fP (0 0 0) Shift the geometrical center to (x,y,z) .TP .B \fB\-aligncenter\fP (0 0 0) Center of rotation for alignment .TP .B \fB\-align\fP (0 0 0) Align to target vector .TP .B \fB\-translate\fP (0 0 0) Translation .TP .B \fB\-rotate\fP (0 0 0) Rotation around the X, Y and Z axes in degrees .TP .B \fB\-[no]princ\fP (no) Orient molecule(s) along their principal axes .TP .B \fB\-scale\fP (1 1 1) Scaling factor .TP .B \fB\-density\fP (1000) Density (g/L) of the output box achieved by scaling .TP .B \fB\-[no]pbc\fP (no) Remove the periodicity (make molecule whole again) .TP .B \fB\-resnr\fP (\-1) Renumber residues starting from resnr .TP .B \fB\-[no]grasp\fP (no) Store the charge of the atom in the B\-factor field and the radius of the atom in the occupancy field .TP .B \fB\-rvdw\fP (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 .TP .B \fB\-[no]sig56\fP (no) Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 .TP .B \fB\-[no]vdwread\fP (no) Read the Van der Waals radii from the file \fBvdwradii.dat\fP rather than computing the radii based on the force field .TP .B \fB\-[no]atom\fP (no) Force B\-factor attachment per atom .TP .B \fB\-[no]legend\fP (no) Make B\-factor legend .TP .B \fB\-label\fP (A) Add chain label for all residues .TP .B \fB\-[no]conect\fP (no) Add CONECT records to a \fI\%\&.pdb\fP file when written. Can only be done when a topology is present .UNINDENT .SH KNOWN ISSUES .INDENT 0.0 .IP \(bu 2 For complex molecules, the periodicity removal routine may break down, .IP \(bu 2 in that case you can use \fI\%gmx trjconv\fP\&. .UNINDENT .SH SEE ALSO .sp \fBgmx(1)\fP .sp More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>. .SH COPYRIGHT 2024, GROMACS development team .\" Generated by docutils manpage writer. .