gmx-helix man page
gmx-helix — Calculate basic properties of alpha helices
gmx 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:
- Helix radius (file radius.xvg). This is merely the RMS deviation in two dimensions for all Calpha atoms. it is calculated as sqrt((sum_i (x^2(i)+y^2(i)))/N) where N is the number of backbone atoms. For an ideal helix the radius is 0.23 nm.
- 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.
- 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.
- 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).
- Helix dipole, backbone only (file dip-ahx.xvg).
- RMS deviation from ideal helix, calculated for the Calpha atoms only (file rms-ahx.xvg).
- Average Calpha - Calpha dihedral angle (file phi-ahx.xvg).
- Average phi and psi angles (file phipsi.xvg).
- Ellipticity at 222 nm according to Hirst and Brooks.
Options to specify input files:
- -s [<.tpr>] (topol.tpr)
Portable xdr run input file
- -n [<.ndx>] (index.ndx)
- -f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
Options to specify output files:
- -cz [<.gro/.g96/...>] (zconf.gro)
Structure file: gro g96 pdb brk ent esp
- -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
- -[no]ev (no)
Write a new 'trajectory' file for ED
- -ahxstart <int> (0)
First residue in helix
- -ahxend <int> (0)
Last residue in helix
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2017, GROMACS development team