Man page - gmx-helix(1)
Packages contas this manual
- gmx-wham(1)
- gmx-trjcat(1)
- gmx-confrms(1)
- gmx_d(1)
- gmx-xpm2ps(1)
- gmx-make_edi(1)
- gmx-solvate(1)
- gmx-awh(1)
- gmx-help(1)
- gmx-hydorder(1)
- gmx-velacc(1)
- gmx-order(1)
- gmx-clustsize(1)
- gmx-densorder(1)
- gmx-msd(1)
- gmx-saxs-legacy(1)
- gmx-covar(1)
- gmx-tcaf(1)
- gmx-filter(1)
- gmx-rms(1)
- gmx-bundle(1)
- gmx-vanhove(1)
- gmx-enemat(1)
- gmx-rama(1)
- gmx-spatial(1)
- gmx-nmens(1)
- gmx-mdmat(1)
- gmx-rotmat(1)
- gmx(1)
- gmx-eneconv(1)
- gmx-h2order(1)
- gmx-current(1)
- gmx-genion(1)
- gmx-rmsdist(1)
- gmx-report-methods(1)
- gmx-distance(1)
- gmx-insert-molecules(1)
- demux(1)
- gmx-dielectric(1)
- gmx-sans-legacy(1)
- gmx-sigeps(1)
- gmx-genrestr(1)
- gmx-analyze(1)
- gmx-convert-tpr(1)
- gmx-potential(1)
- gmx-wheel(1)
- gmx-mk_angndx(1)
- gmx-x2top(1)
- gmx-genconf(1)
- gmx-mindist(1)
- gmx-dipoles(1)
- gmx-polystat(1)
- gmx-hbond-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-make_ndx(1)
- gmx-nonbonded-benchmark(1)
- gmx-sham(1)
- gmx-nmr(1)
- xplor2gmx(1)
- gmx-densmap(1)
- gmx-bar(1)
- gmx-trajectory(1)
- gmx-sasa(1)
- gmx-dos(1)
- gmx-principal(1)
- gmx-pme_error(1)
- gmx-hbond(1)
- gmx-dump(1)
- gmx-traj(1)
- gmx-freevolume(1)
- gmx-trjconv(1)
- gmx_mpi(1)
- gmx-density(1)
- gmx-pdb2gmx(1)
- gmx-spol(1)
- gmx-cluster(1)
- gmx-select(1)
- gmx-rmsf(1)
- gmx-angle(1)
- gmx-saltbr(1)
- gmx-scattering(1)
- gmx-energy(1)
- gmx-dyecoupl(1)
- gmx-disre(1)
- gmx-pairdist(1)
- gmx-extract-cluster(1)
- gmx-tune_pme(1)
- gmx-check(1)
- gmx-nmtraj(1)
- gmx-helix(1)
- gmx-trjorder(1)
- gmx-grompp(1)
- gmx-gangle(1)
- gmx-dssp(1)
- gmx-convert-trj(1)
- gmx-sorient(1)
- gmx-chi(1)
- gmx-anaeig(1)
- gmx-lie(1)
- gmx-helixorient(1)
- gmx-mdrun(1)
- gmx-editconf(1)
- gmx-rdf(1)
- gmx_mpi_d(1)
- gmx-rotacf(1)
- gmx-nmeig(1)
- gmx-gyrate(1)
Package: gromacs-data
apt-get install gromacs-data
apt-get install gromacs-data
Manuals in package:
Documentations in package:
Manual
| GMX-HELIX(1) | GROMACS | GMX-HELIX(1) |
NAME
gmx-helix - Calculate basic properties of alpha helices
SYNOPSIS
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>]
DESCRIPTION
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
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
SEE ALSO
gmx(1)
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2025, GROMACS development team
| May 12, 2025 | 2025.2 |