g_editconf_d (1) - Linux Manuals

g_editconf_d: edits the box and writes subgroups

NAME

editconf - edits the box and writes subgroups

VERSION 4.0.1

SYNOPSIS

editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf bfact.dat -[no]h -nice int -[no]w -[no]ndef -bt enum -box vector -angles vector -d real -[no]c -center vector -translate vector -rotate vector -[no]princ -scale vector -density real -[no]vol -[no]pbc -[no]grasp -rvdw real -sig56 real -[no]vdwread -[no]atom -[no]legend -label string

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 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.

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 tpb tpa 

-n index.ndx Input, Opt.
 Index file 

-o out.gro Output, Opt.
 Structure file: gro g96 pdb 

-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

-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

-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]volyes
 Compute and print volume of the box

-[no]pbcno
 Remove the periodicity (make molecule whole again)

-[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

KNOWN PROBLEMS

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