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gmx-helix(1) GROMACS Manual gmx-helix(1)
NAME
gmx-helix - Calculate basic properties of alpha helices
SYNOPSIS
gmx helix [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-f [<.xtc/.trr/...>]] [-cz [<.gro/.g96/...>]]
[-nice <int>] [-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 proper‐
ties are computed:
1. 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
(x2(i)+y2(i)))/N) where N is the number of backbone atoms. For an ideal
helix the radius is 0.23 nm 2. 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. 3. 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 4. 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). 5. Helix dipole, backbone only (file dip-ahx.xvg). 6. RMS
deviation from ideal helix, calculated for the Calpha atoms only (file
rms-ahx.xvg). 7. Average Calpha - Calpha dihedral angle (file
phi-ahx.xvg). 8. Average phi and psi angles (file phipsi.xvg). 9.
Ellipticity at 222 nm according to Hirst and Brooks.
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input)
Index file
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-cz [<.gro/.g96/...>] (zconf.gro) (Output)
Structure file: gro g96 pdb brk ent esp
Other options:
-nice <int> (19)
Set the nicelevel
-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
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6 gmx-helix(1)
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