gmx editconf#

Synopsis#

gmx editconf [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-bf [<.dat>]]
             [-o [<.gro/.g96/...>]] [-mead [<.pqr>]] [-[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>] [-[no]sig56] [-[no]vdwread] [-[no]atom]
             [-[no]legend] [-label <string>] [-[no]conect]

Description#

gmx 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. The -center option can be used to shift the geometric center of the system from the default of (x/2, y/2, z/2) implied by -c to some other value.

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 the number of B-factors is larger than the number of the 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:

gmx 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.

Options#

Options to specify input files:

-f [<.gro/.g96/…>] (conf.gro): Structure file: gro g96 pdb brk ent esp tpr
-n [<.ndx>] (index.ndx) (Optional): Index file
-bf [<.dat>] (bfact.dat) (Optional): Generic data file

Options to specify output files:

-o [<.gro/.g96/…>] (out.gro) (Optional): Structure file: gro g96 pdb brk ent esp
-mead [<.pqr>] (mead.pqr) (Optional): Coordinate file for MEAD

Other options:

-[no]w (no): View output .xvg, .xpm, .eps and .pdb files
-[no]ndef (no): Choose output from default index groups
-bt <enum> (triclinic): Box type for -box and -d: triclinic, cubic, dodecahedron, 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 (no): Center molecule in box (implied by -box and -d)
-center <vector> (0 0 0): Shift the geometrical center to (x,y,z)
-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]princ (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]pbc (no): Remove the periodicity (make molecule whole again)
-resnr <int> (-1): Renumber residues starting from resnr
-[no]grasp (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
-[no]sig56 (no): Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-[no]vdwread (no): Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-[no]atom (no): Force B-factor attachment per atom
-[no]legend (no): Make B-factor legend
-label <string> (A): Add chain label for all residues
-[no]conect (no): Add CONECT records to a .pdb file when written. Can only be done when a topology is present

Known Issues#

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