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)