g_helix(1) - Linux man page
Name
g_helix - calculates basic properties of alpha helicesVERSION 4.5.4-dev-20110404-bc5695c
Synopsis
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 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 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. 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.
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/>.