g_helix_d (1) - Linux Man Pages
g_helix_d: calculates basic properties of alpha helices
NAMEg_helix - calculates basic properties of alpha helices
SYNOPSISg_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
DESCRIPTIONg_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
-nice int 19
-b time 0
-e time 0
-dt time 0
-r0 int 1
-prop enum RAD
-ahxstart int 0
-ahxend int 0
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