g_helix(1)

NAME
g_helix - calculates basic properties of alpha helices VERSION 4.5.4-dev-20110404-bc5695c

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

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/>.