Man page - gmx-helix(1)
Packages contains this manual
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- gmx-energy(1)
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- gmx-gangle(1)
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- gmx-grompp(1)
- gmx-make_edi(1)
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- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
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- demux(1)
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- gmx-saxs-legacy(1)
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- gmx-mdmat(1)
- xplor2gmx(1)
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- gmx-dssp(1)
- gmx-densorder(1)
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- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-HELIX
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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 (xˆ2(i)+yˆ2(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