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gmx-helix - Online in the Cloud

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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

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