NAMEeditconf - edits the box and writes subgroups VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSISeditconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf bfact.dat -[no]h -[no]version -nice int -[no]w -[no]ndef -bt enum -box vector -angles vector -d real -[no]c -center vector -aligncenter vector -align vector -translate vector -rotate vector -[no]princ -scale vector -density real -[no]pbc -resnr int -[no]grasp -rvdw real -sig56 real -[no]vdwread -[no]atom -[no]legend -label string -[no]conect
DESCRIPTIONeditconf 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: 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)/2.
FILES-f conf.gro Input Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -o out.gro Output, Opt. Structure file: gro g96 pdb etc. -mead mead.pqr Output, Opt. Coordinate file for MEAD -bf bfact.dat Input, Opt. Generic data file
OTHER OPTIONS-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -[no]wno View output .xvg, .xpm, .eps and .pdb files -[no]ndefno Choose output from default index groups -bt enum triclinic Box type for -box and -d: triclinic, cubic, dodecahedron or octahedron -box vector 0 0 0 Box vector lengths (a,b,c) -angles vector 90 90 90 Angles between the box vectors (bc,ac,ab) -d real 0 Distance between the solute and the box -[no]cno Center molecule in box (implied by -box and -d) -center vector 0 0 0 Coordinates of geometrical center -aligncenter vector 0 0 0 Center of rotation for alignment -align vector 0 0 0 Align to target vector -translate vector 0 0 0 Translation -rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees -[no]princno Orient molecule(s) along their principal axes -scale vector 1 1 1 Scaling factor -density real 1000 Density (g/L) of the output box achieved by scaling -[no]pbcno Remove the periodicity (make molecule whole again) -resnr int -1 Renumber residues starting from resnr -[no]graspno Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field -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 -sig56 real 0 Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 -[no]vdwreadno Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field -[no]atomno Force B-factor attachment per atom -[no]legendno Make B-factor legend -label string A Add chain label for all residues -[no]conectno Add CONECT records to a .pdb file when written. Can only be done when a topology is present
KNOWN PROBLEMS- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv.
SEE ALSOgromacs(7) More information about GROMACS is available at <//www.gromacs.org/>. Mon 4 Apr 2011 EDITCONF(1)