# g_editconf_d (1) - Linux Man Pages

## g_editconf_d: edits the box and writes subgroups

## NAME

editconf - edits the box and writes subgroups## 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**

**-n*** index.ndx*
**Input, Opt.**

**-o*** out.gro*
**Output, Opt.**

**-mead*** mead.pqr*
**Output, Opt.**

**-bf*** bfact.dat*
**Input, Opt.**

## OTHER OPTIONS

**-[no]h**

*no*

**-nice*** int*** 0**

**-[no]w***no *

**-[no]ndef***no *

**-bt*** enum*** triclinic**

** triclinic**,

**,**cubic

dodecahedron

octahedron

**-box*** vector*** 0 0 0**

**-angles*** vector*** 90 90 90**

**-d*** real*** 0 **

**-[no]c***no *

**-center*** vector*** 0 0 0**

**-translate*** vector*** 0 0 0**

**-rotate*** vector*** 0 0 0**

**-[no]princ***no *

**-scale*** vector*** 1 1 1**

**-density*** real*** 1000 **

**-[no]vol***yes *

**-[no]pbc***no *

**-[no]grasp***no *

**-rvdw*** real*** 0.12 **

**-sig56*** real*** 0 **

**-[no]vdwread***no *

**-[no]atom***no *

**-[no]legend***no *

**-label*** string*** A**