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)
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)-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