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.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
RMS deviation from ideal helix, calculated for the Calpha atoms only (file
Average Calpha - Calpha dihedral angle (file
Average phi and psi angles (file
Ellipticity at 222 nm according to Hirst and Brooks.
Options to specify input files:
Portable xdr run input file
Options to specify output files:
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
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
Write a new ‘trajectory’ file for ED
First residue in helix
Last residue in helix