Provided by: gromacs-data_2019.3-2_all
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 Other options: -b <time> (0) Time of first frame to read from trajectory (default unit ps) -e <time> (0) Time of last frame to read from trajectory (default unit ps) -dt <time> (0) Only use frame when t MOD dt = first time (default unit 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
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
2019, GROMACS development team