gmx-helix - Calculate basic properties of alpha helices

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                      GMX-HELIX(1)

gmxhelix  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.

       gmx-helix - Calculate basic properties of alpha helices

       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: xtctrrcptgrog96pdbtng

       Options to specify output files:

       -cz[<.gro/.g96/...>](zconf.gro)
              Structure file: grog96pdb 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

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          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>]