EnglishFrenchSpanish

Ad


OnWorks favicon

gmx-helix - Online in the Cloud

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

This is the command gmx-helix 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-helix - Calculate basic properties of alpha helices

SYNOPSIS


gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
[-cz [<.gro/.g96/...>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-r0 <int>] [-[no]q] [-[no]F]
[-[no]db] [-[no]ev] [-ahxstart <int>] [-ahxend <int>]

DESCRIPTION


gmx helix computes all kinds of helix properties. First, the peptide is checked to find
the longest helical part, as determined by hydrogen bonds and phi/psi angles. That bit is
fitted to an ideal helix around the z-axis and centered around the origin. Then the
following properties are computed:

· Helix radius (file radius.xvg). This is merely the RMS deviation in two dimensions
for all Calpha atoms. it is calculated as sqrt((sum_i (x^2(i)+y^2(i)))/N) where N is
the number of backbone atoms. For an ideal helix the radius is 0.23 nm.

· Twist (file twist.xvg). The average helical angle per residue is calculated. For an
alpha-helix it is 100 degrees, for 3-10 helices it will be smaller, and for 5-helices
it will be larger.

· Rise per residue (file rise.xvg). The helical rise per residue is plotted as the
difference in z-coordinate between Calpha atoms. For an ideal helix, this is 0.15 nm.

· Total helix length (file len-ahx.xvg). The total length of the helix in nm. This is
simply the average rise (see above) times the number of helical residues (see below).

· Helix dipole, backbone only (file dip-ahx.xvg).

· RMS deviation from ideal helix, calculated for the Calpha atoms only (file
rms-ahx.xvg).

· Average Calpha - Calpha dihedral angle (file phi-ahx.xvg).

· Average phi and psi angles (file phipsi.xvg).

· Ellipticity at 222 nm according to Hirst and Brooks.

OPTIONS


Options to specify input files:

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

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

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

Options to specify output files:

-cz [<.gro/.g96/...>] (zconf.gro)
Structure file: gro g96 pdb brk ent esp

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)

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-r0 <int> (1)
The first residue number in the sequence

-[no]q (no)
Check at every step which part of the sequence is helical

-[no]F (yes)
Toggle fit to a perfect helix

-[no]db (no)
Print debug info

-[no]ev (no)
Write a new 'trajectory' file for ED

-ahxstart <int> (0)
First residue in helix

-ahxend <int> (0)
Last residue in helix

Use gmx-helix online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    NSIS: Nullsoft Scriptable Install System
    NSIS: Nullsoft Scriptable Install System
    NSIS (Nullsoft Scriptable Install
    System) is a professional open source
    system to create Windows installers. It
    is designed to be as small and flexible
    as possi...
    Download NSIS: Nullsoft Scriptable Install System
  • 2
    authpass
    authpass
    AuthPass is an open source password
    manager with support for the popular and
    proven Keepass (kdbx 3.x AND kdbx 4.x ...
    Download authpass
  • 3
    Zabbix
    Zabbix
    Zabbix is an enterprise-class open
    source distributed monitoring solution
    designed to monitor and track
    performance and availability of network
    servers, device...
    Download Zabbix
  • 4
    KDiff3
    KDiff3
    This repository is no longer maintained
    and is kept for archival purposes. See
    https://invent.kde.org/sdk/kdiff3 for
    the newest code and
    https://download.kde.o...
    Download KDiff3
  • 5
    USBLoaderGX
    USBLoaderGX
    USBLoaderGX is a GUI for
    Waninkoko's USB Loader, based on
    libwiigui. It allows listing and
    launching Wii games, Gamecube games and
    homebrew on Wii and WiiU...
    Download USBLoaderGX
  • 6
    Firebird
    Firebird
    Firebird RDBMS offers ANSI SQL features
    & runs on Linux, Windows &
    several Unix platforms. Features
    excellent concurrency & performance
    & power...
    Download Firebird
  • More »

Linux commands

Ad