g_helix(1) calculates basic properties of alpha helices


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


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.


-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. 


 Print help info and quit

 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)

 View output  .xvg .xpm .eps and  .pdb files

-r0 int 1
 The first residue number in the sequence

 Check at every step which part of the sequence is helical

 Toggle fit to a perfect helix

 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

 Write a new 'trajectory' file for ED

-ahxstart int 0
 First residue in helix

-ahxend int 0
 Last residue in helix