g_helix(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					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 num-
       ber 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/>.

								  Mon 4 Apr 2011							g_helix(1)