NAME
g_helix - calculates basic properties of alpha helices
VERSION 4.0.1
SYNOPSIS
g_helix -s topol.tpr -n index.ndx -f traj.xtc -to gtraj.g87 -cz
zconf.gro -co waver.gro -[no]h -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 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(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 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
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
-co waver.gro Output
Structure file: gro g96 pdb
OTHER OPTIONS
-[no]hno
Print help 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/>.
Thu 16 Oct 2008 g_helix(1)