Main Table of Contents

Thu 26 Aug 2010


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

Other options

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