gmx-helix man page
gmx-helix — Calculate basic properties of alpha helices
gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
[-cz [<.gro/.g96/...>]] [-b <time>] [-e <time>]
[-dt <time>] [-[no]w] [-r0 <int>] [-[no]q] [-[no]F]
[-[no]db] [-[no]ev] [-ahxstart <int>] [-ahxend <int>]
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)
- Index file
- -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