Manual:editconf 3.3.2
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[edit] Description
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.
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. The volume of a dodecahedron is 0.71 and that of a truncated
octahedron is 0.77 of that of a cubic box with the same periodic image
distance.
Option -box requires only one value for a cubic box,
dodecahedron and a truncated octahedron.
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 can not 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, 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
can be scaled to give a certain density (option
-density). A special feature of the scaling option,
when the factor -1 is given in one dimension, one obtains a mirror image,
mirrored in one of the plains, 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 sizes 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.
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.
[edit] Known Problems
- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
[edit] Files
Option Filename Type Description ----------------------------------------------------- -f conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -o out.gro Output, Opt. Generic structure: gro g96 pdb xml -mead mead.pqr Output, Opt. Coordinate file for MEAD -bf bfact.dat Input, Opt. Generic data file
[edit] Options
Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]w bool no View output xvg, xpm, eps and pdb files -[no]ndef bool no 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]c bool no Center molecule in box (implied by -box and -d) -center vector 0 0 0 Coordinates of geometrical center -translate vector 0 0 0 Translation -rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees -[no]princ bool no 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]vol bool yes Compute and print volume of the box -[no]pbc bool no Remove the periodicity (make molecule whole again) -[no]grasp bool no 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]vdwread bool no Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field -[no]atom bool no Force B-factor attachment per atom -[no]legend bool no Make B-factor legend -label string A Add chain label for all residues
