editconf Main Table of Contents

VERSION 4.5 Thu 26 Aug 2010

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, 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. 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 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, 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.

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

Other options

Known problems

• For complex molecules, the periodicity removal routine may break down,
• in that case you can use trjconv.