gmx helix¶
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:
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