g_helix(1)
NAME
g_helix - calculates everything you want to know about helices
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
- Generic run input: tpr tpb tpa xml
- -n index.ndx Input
- Index file
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -to gtraj.g87 Output, Opt.
- Gromos-87 ASCII trajectory format
- -cz zconf.gro Output
- Generic structure: gro g96 pdb xml
- -co waver.gro Output
- Generic structure: gro g96 pdb xml
OTHER OPTIONS
- -[no]h no
- 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]w no
- View output xvg, xpm, eps and pdb files
- -r0 int 1
- The first residue number in the sequence
- -[no]q no
- Check at every step which part of the sequence is helical
- -[no]F yes
- Toggle fit to a perfect helix
- -[no]db no
- 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]ev no
- Write a new 'trajectory' file for ED
- -ahxstart int 0
- First residue in helix
- -ahxend int 0
- Last residue in helix
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.