NAME

       g_helix - calculates basic properties of alpha helices

       VERSION 4.6.5

SYNOPSIS

       g_helix  -s  topol.tpr  -n  index.ndx  -f  traj.xtc  -to  gtraj.g87  -cz  zconf.gro  -co waver.gro -[no]h
       -[no]version -nice int -b time -e time -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop  enum  -[no]ev
       -ahxstart int -ahxend int

DESCRIPTION

         g_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:

         1.  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 (x2(i)+y2(i)))/N) where N is the number of backbone atoms. For an
       ideal helix the radius is 0.23 nm

        2. 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.

         3.  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

        4. 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).

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

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

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

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

        9. Ellipticity at 222 nm according to Hirst and Brooks.

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input
        Index file

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -to gtraj.g87 Output, Opt.
        Gromos-87 ASCII trajectory format

       -cz zconf.gro Output
        Structure file: gro g96 pdb etc.

       -co waver.gro Output
        Structure file: gro g96 pdb etc.

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -r0 int 1
        The first residue number in the sequence

       -[no]qno
        Check at every step which part of the sequence is helical

       -[no]Fyes
        Toggle fit to a perfect helix

       -[no]dbno
        Print debug info

       -prop enum RAD
        Select  property  to  weight  eigenvectors  with. WARNING experimental stuff:  RAD,  TWIST,  RISE,  LEN,
       NHX,  DIP,  RMS,  CPHI,  RMSA,  PHI,  PSI,  HB3,  HB4,  HB5 or  CD222

       -[no]evno
        Write a new 'trajectory' file for ED

       -ahxstart int 0
        First residue in helix

       -ahxend int 0
        Last residue in helix

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       g_helix(1)