gmx helix#


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>]


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 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)

Time of first frame to read from trajectory (default unit ps)

-e <time> (0)

Time of last frame to read from trajectory (default unit ps)

-dt <time> (0)

Only use frame when t MOD dt = first time (default unit 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