EnglishFrenchSpanish

OnWorks favicon

gmx-helixorient - Online in the Cloud

Run gmx-helixorient in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-helixorient that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-helixorient - Calculate local pitch/bending/rotation/orientation inside helices

SYNOPSIS


gmx helixorient [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-oaxis [<.dat>]] [-ocenter [<.dat>]] [-orise [<.xvg>]]
[-oradius [<.xvg>]] [-otwist [<.xvg>]]
[-obending [<.xvg>]] [-otilt [<.xvg>]] [-orot [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
[-[no]sidechain] [-[no]incremental]

DESCRIPTION


gmx helixorient calculates the coordinates and direction of the average axis inside an
alpha helix, and the direction/vectors of both the Calpha and (optionally) a sidechain
atom relative to the axis.

As input, you need to specify an index group with Calpha atoms corresponding to an
alpha-helix of continuous residues. Sidechain directions require a second index group of
the same size, containing the heavy atom in each residue that should represent the
sidechain.

Note that this program does not do any fitting of structures.

We need four Calpha coordinates to define the local direction of the helix axis.

The tilt/rotation is calculated from Euler rotations, where we define the helix axis as
the local x-axis, the residues/Calpha vector as y, and the z-axis from their cross
product. We use the Euler Y-Z-X rotation, meaning we first tilt the helix axis (1) around
and (2) orthogonal to the residues vector, and finally apply the (3) rotation around it.
For debugging or other purposes, we also write out the actual Euler rotation angles as
theta[1-3].xvg

OPTIONS


Options to specify input files:

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-oaxis [<.dat>] (helixaxis.dat)
Generic data file

-ocenter [<.dat>] (center.dat)
Generic data file

-orise [<.xvg>] (rise.xvg)
xvgr/xmgr file

-oradius [<.xvg>] (radius.xvg)
xvgr/xmgr file

-otwist [<.xvg>] (twist.xvg)
xvgr/xmgr file

-obending [<.xvg>] (bending.xvg)
xvgr/xmgr file

-otilt [<.xvg>] (tilt.xvg)
xvgr/xmgr file

-orot [<.xvg>] (rotation.xvg)
xvgr/xmgr file

Other options:

-b <time> (0)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-[no]sidechain (no)
Calculate sidechain directions relative to helix axis too.

-[no]incremental (no)
Calculate incremental rather than total rotation/tilt.

Use gmx-helixorient online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

Linux commands

  • 1
    abiword
    abiword
    abiword � flexible cross-platform word
    processor ...
    Run abiword
  • 2
    abl
    abl
    abl - Prefixed representation for
    boolean functions DESCRIPTION:
    libablmmm.a is a library that enables to
    represent a boolean function in a
    LISP-like form. An ...
    Run abl
  • 3
    cpan2debp
    cpan2debp
    dh-make-perl - Create debian source
    packages from Perl modules ...
    Run cpan2debp
  • 4
    cpan2distp
    cpan2distp
    cpan2dist - The CPANPLUS distribution
    creator DESCRIPTION: This script will
    create distributions of "CPAN" modules
    of the format you specify, including its
    pre...
    Run cpan2distp
  • 5
    gbp-buildpackage
    gbp-buildpackage
    gbp-buildpackage - Build Debian
    packages from a Git repository ...
    Run gbp-buildpackage
  • 6
    gbp-clone
    gbp-clone
    gbp-clone - Clone a repository from
    remote ...
    Run gbp-clone
  • More »

Ad