1g_helixorient(1)          GROMACS suite, VERSION 4.5          g_helixorient(1)
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NAME

6       g_helixorient  -  calculates  local  pitch/bending/rotation/orientation
7       inside helices
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9       VERSION 4.5
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SYNOPSIS

12       g_helixorient -s topol.tpr  -f  traj.xtc  -n  index.ndx  -oaxis  helix‐
13       axis.dat   -ocenter  center.dat  -orise  rise.xvg  -oradius  radius.xvg
14       -otwist twist.xvg -obending bending.xvg  -otilt  tilt.xvg  -orot  rota‐
15       tion.xvg  -[no]h  -[no]version  -nice int -b time -e time -dt time -xvg
16       enum -[no]sidechain -[no]incremental
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DESCRIPTION

19       g_helixorient calculates the coordinates and direction of  the  average
20       axis inside an alpha helix, and the direction/vectors of both the alpha
21       carbon and (optionally) a sidechain atom relative to the axis.
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24       As input, you need to specify an index group with  alpha  carbon  atoms
25       corresponding  to  an  alpha  helix  of  continuous residues. Sidechain
26       directions require a second index group of the  same  size,  containing
27       the heavy atom in each residue that should represent the sidechain.
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30       Note that this program does not do any fitting of structures.
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33       We  need  four  Calpha coordinates to define the local direction of the
34       helix axis.
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37       The tilt/rotation is calculated from Euler rotations, where  we  define
38       the  helix  axis  as the local X axis, the residues/CA-vector as Y, and
39       the Z axis from their cross product. We use the Euler  Y-Z-X  rotation,
40       meaning  we  first tilt the helix axis (1) around and (2) orthogonal to
41       the residues vector, and finally apply the (3) rotation around it.  For
42       debugging  or  other purposes, we also write out the actual Euler rota‐
43       tion angles as theta1-3.xvg
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FILES

46       -s topol.tpr Input
47        Run input file: tpr tpb tpa
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49       -f traj.xtc Input
50        Trajectory: xtc trr trj gro g96 pdb cpt
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52       -n index.ndx Input, Opt.
53        Index file
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55       -oaxis helixaxis.dat Output
56        Generic data file
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58       -ocenter center.dat Output
59        Generic data file
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61       -orise rise.xvg Output
62        xvgr/xmgr file
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64       -oradius radius.xvg Output
65        xvgr/xmgr file
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67       -otwist twist.xvg Output
68        xvgr/xmgr file
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70       -obending bending.xvg Output
71        xvgr/xmgr file
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73       -otilt tilt.xvg Output
74        xvgr/xmgr file
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76       -orot rotation.xvg Output
77        xvgr/xmgr file
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OTHER OPTIONS

81       -[no]hno
82        Print help info and quit
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84       -[no]versionno
85        Print version info and quit
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87       -nice int 19
88        Set the nicelevel
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90       -b time 0
91        First frame (ps) to read from trajectory
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93       -e time 0
94        Last frame (ps) to read from trajectory
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96       -dt time 0
97        Only use frame when t MOD dt = first time (ps)
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99       -xvg enum xmgrace
100        xvg plot formatting:  xmgrace,  xmgr or  none
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102       -[no]sidechainno
103        Calculate sidechain directions relative to helix axis too.
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105       -[no]incrementalno
106        Calculate incremental rather than total rotation/tilt.
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SEE ALSO

110       gromacs(7)
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112       More  information  about  GROMACS  is  available  at   <http://www.gro‐
113       macs.org/>.
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117                                Thu 26 Aug 2010               g_helixorient(1)
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