1GMX-HELIXORIENT(1) GROMACS GMX-HELIXORIENT(1)
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6 gmx-helixorient - Calculate local pitch/bending/rotation/orientation
7 inside helices
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10 gmx helixorient [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
11 [-oaxis [<.dat>]] [-ocenter [<.dat>]] [-orise [<.xvg>]]
12 [-oradius [<.xvg>]] [-otwist [<.xvg>]]
13 [-obending [<.xvg>]] [-otilt [<.xvg>]] [-orot [<.xvg>]]
14 [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
15 [-[no]sidechain] [-[no]incremental]
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18 gmx helixorient calculates the coordinates and direction of the average
19 axis inside an alpha helix, and the direction/vectors of both the Cal‐
20 pha and (optionally) a sidechain atom relative to the axis.
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22 As input, you need to specify an index group with Calpha atoms corre‐
23 sponding to an alpha-helix of continuous residues. Sidechain directions
24 require a second index group of the same size, containing the heavy
25 atom in each residue that should represent the sidechain.
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27 Note that this program does not do any fitting of structures.
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29 We need four Calpha coordinates to define the local direction of the
30 helix axis.
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32 The tilt/rotation is calculated from Euler rotations, where we define
33 the helix axis as the local x-axis, the residues/Calpha vector as y,
34 and the z-axis from their cross product. We use the Euler Y-Z-X rota‐
35 tion, meaning we first tilt the helix axis (1) around and (2) orthogo‐
36 nal to the residues vector, and finally apply the (3) rotation around
37 it. For debugging or other purposes, we also write out the actual Euler
38 rotation angles as theta[1-3].xvg
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41 Options to specify input files:
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43 -s [<.tpr>] (topol.tpr)
44 Portable xdr run input file
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46 -f [<.xtc/.trr/…>] (traj.xtc)
47 Trajectory: xtc trr cpt gro g96 pdb tng
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49 -n [<.ndx>] (index.ndx) (Optional)
50 Index file
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52 Options to specify output files:
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54 -oaxis [<.dat>] (helixaxis.dat)
55 Generic data file
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57 -ocenter [<.dat>] (center.dat)
58 Generic data file
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60 -orise [<.xvg>] (rise.xvg)
61 xvgr/xmgr file
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63 -oradius [<.xvg>] (radius.xvg)
64 xvgr/xmgr file
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66 -otwist [<.xvg>] (twist.xvg)
67 xvgr/xmgr file
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69 -obending [<.xvg>] (bending.xvg)
70 xvgr/xmgr file
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72 -otilt [<.xvg>] (tilt.xvg)
73 xvgr/xmgr file
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75 -orot [<.xvg>] (rotation.xvg)
76 xvgr/xmgr file
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78 Other options:
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80 -b <time> (0)
81 Time of first frame to read from trajectory (default unit ps)
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83 -e <time> (0)
84 Time of last frame to read from trajectory (default unit ps)
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86 -dt <time> (0)
87 Only use frame when t MOD dt = first time (default unit ps)
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89 -xvg <enum> (xmgrace)
90 xvg plot formatting: xmgrace, xmgr, none
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92 -[no]sidechain (no)
93 Calculate sidechain directions relative to helix axis too.
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95 -[no]incremental (no)
96 Calculate incremental rather than total rotation/tilt.
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99 gmx(1)
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101 More information about GROMACS is available at <‐
102 http://www.gromacs.org/>.
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105 2019, GROMACS development team
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1102019.4 Oct 02, 2019 GMX-HELIXORIENT(1)