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.