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       g_helix - calculates basic properties of alpha helices

       VERSION 4.0.1


       g_helix  -s  topol.tpr  -n  index.ndx  -f  traj.xtc  -to  gtraj.g87 -cz
       zconf.gro -co waver.gro -[no]h -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


       g_helix computes all kind of helix properties. First,  the  peptide  is
       checked  to  find  the  longest  helical  part.  This  is 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  calced 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 alpha helix it is 100 degrees, for 3-10 helices it will
       be smaller, 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  Ca  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. Number of helical residues (file n-ahx.xvg). The title says it all.

        6. Helix Dipole, backbone only (file dip-ahx.xvg).

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

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

        9. Average Phi and Psi angles (file phipsi.xvg).

        10. Ellipticity at 222 nm according to  Hirst and Brooks


       -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

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


        Print help 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)

        View output xvg, xpm, eps and pdb files

       -r0 int 1
        The first residue number in the sequence

        Check at every step which part of the sequence is helical

        Toggle fit to a perfect helix

        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

        Write a new ’trajectory’ file for ED

       -ahxstart int 0
        First residue in helix

       -ahxend int 0
        Last residue in helix



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                     g_helix(1)