.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME editconf - edits the box and writes subgroups .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3editconf\fP .BI "\-f" " conf.gro " .BI "\-n" " index.ndx " .BI "\-o" " out.gro " .BI "\-mead" " mead.pqr " .BI "\-bf" " bfact.dat " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-[no]w" "" .BI "\-[no]ndef" "" .BI "\-bt" " enum " .BI "\-box" " vector " .BI "\-angles" " vector " .BI "\-d" " real " .BI "\-[no]c" "" .BI "\-center" " vector " .BI "\-aligncenter" " vector " .BI "\-align" " vector " .BI "\-translate" " vector " .BI "\-rotate" " vector " .BI "\-[no]princ" "" .BI "\-scale" " vector " .BI "\-density" " real " .BI "\-[no]pbc" "" .BI "\-resnr" " int " .BI "\-[no]grasp" "" .BI "\-rvdw" " real " .BI "\-sig56" " real " .BI "\-[no]vdwread" "" .BI "\-[no]atom" "" .BI "\-[no]legend" "" .BI "\-label" " string " .BI "\-[no]conect" "" .SH DESCRIPTION \&\fB 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: \fB triclinic\fR is a \&triclinic box, \fB cubic\fR is a rectangular box with all sides equal \&\fB dodecahedron\fR represents a rhombic dodecahedron and \&\fB octahedron\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 \fB triclinic\fR box the size of the system in the \fI x\fR\-, \fI y\fR\-, \&and \fI z\fR\-directions is used. With \fB \-d\fR and \fB cubic\fR, \&\fB dodecahedron\fR or \fB octahedron\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 \fI x\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, \fB editconf\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: \&\fB editconf \-f in \-rotate 0 45 35.264 \-bt o \-box veclen \-o out\fR \&where \fB veclen\fR is the size of the cubic box times sqrt(3)/2. .SH FILES .BI "\-f" " conf.gro" .B Input Structure file: gro g96 pdb tpr etc. .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-o" " out.gro" .B Output, Opt. Structure file: gro g96 pdb etc. .BI "\-mead" " mead.pqr" .B Output, Opt. Coordinate file for MEAD .BI "\-bf" " bfact.dat" .B Input, Opt. Generic data file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 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" " enum" " triclinic" Box type for \-box and \-d: \fB triclinic\fR, \fB cubic\fR, \fB dodecahedron\fR or \fB octahedron\fR .BI "\-box" " vector" " 0 0 0" Box vector lengths (a,b,c) .BI "\-angles" " vector" " 90 90 90" Angles between the box vectors (bc,ac,ab) .BI "\-d" " real" " 0 " Distance between the solute and the box .BI "\-[no]c" "no " Center molecule in box (implied by \-box and \-d) .BI "\-center" " vector" " 0 0 0" Coordinates of geometrical center .BI "\-aligncenter" " vector" " 0 0 0" Center of rotation for alignment .BI "\-align" " vector" " 0 0 0" Align to target vector .BI "\-translate" " vector" " 0 0 0" Translation .BI "\-rotate" " vector" " 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" " vector" " 1 1 1" Scaling factor .BI "\-density" " real" " 1000 " Density (g/L) of the output box achieved by scaling .BI "\-[no]pbc" "no " Remove the periodicity (make molecule whole again) .BI "\-resnr" " int" " \-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" " 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 .BI "\-sig56" " real" " 0 " 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 vdwradii.dat 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" " string" " 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 PROBLEMS \- For complex molecules, the periodicity removal routine may break down, in that case you can use \fB trjconv\fR. .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.