Main Table of Contents

Wed 13 Nov 2013


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 φ/ψ 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 Cα 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
2. Twist (file twist.xvg). The average helical angle per residue is calculated. For an α-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 Cα 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 Cα atoms only (file rms-ahx.xvg).
7. Average Cα - Cα dihedral angle (file phi-ahx.xvg).
8. Average φ and ψ angles (file phipsi.xvg).
9. 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 etc.
-co waver.gro Output Structure file: gro g96 pdb etc.

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no View output .xvg, .xpm, .eps and .pdb files
-r0 int 1 The first residue number in the sequence
-[no]q bool no Check at every step which part of the sequence is helical
-[no]F bool yes Toggle fit to a perfect helix
-[no]db bool no 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]ev bool no Write a new 'trajectory' file for ED
-ahxstart int 0 First residue in helix
-ahxend int 0 Last residue in helix