DragonFly On-Line Manual Pages

gmx-helix(1)                    GROMACS Manual                    gmx-helix(1)

NAME
       gmx-helix - Calculate basic properties of alpha helices

SYNOPSIS
       gmx helix [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                 [-f [<.xtc/.trr/...>]] [-cz [<.gro/.g96/...>]]
                 [-nice <int>] [-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:

       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.

OPTIONS
       Options to specify input and output files:

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

       -n [<.ndx>] (index.ndx) (Input)
           Index file

       -f [<.xtc/.trr/...>] (traj.xtc) (Input)
           Trajectory: xtc trr cpt trj gro g96 pdb tng

       -cz [<.gro/.g96/...>] (zconf.gro) (Output)
           Structure file: gro g96 pdb brk ent esp

       Other options:

       -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]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

SEE ALSO
       gromacs(7)

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

VERSION 5.0.6                                                     gmx-helix(1)