g_helix(1)

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

6       g_helix - calculates basic properties of alpha helices
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8       VERSION 4.5
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SYNOPSIS

11       g_helix  -s  topol.tpr  -n  index.ndx  -f  traj.xtc  -to  gtraj.g87 -cz
12       zconf.gro -co waver.gro -[no]h -[no]version -nice int -b time  -e  time
13       -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop enum -[no]ev -ahxs‐
14       tart int -ahxend int
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DESCRIPTION

17       g_helix computes all kind of helix properties. First,  the  peptide  is
18       checked  to find the longest helical part. This is determined by Hydro‐
19       gen bonds and Phi/Psi angles.  That bit is fitted  to  an  ideal  helix
20       around  the  Z-axis and centered around the origin.  Then the following
21       properties are computed:
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24        1. Helix radius (file radius.xvg). This is merely the RMS deviation in
25       two  dimensions  for  all  Calpha  atoms.   it  is  calced as sqrt((SUM
26       i(x2(i)+y2(i)))/N), where N is the number of  backbone  atoms.  For  an
27       ideal helix the radius is 0.23 nm
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29         2.  Twist  (file twist.xvg). The average helical angle per residue is
30       calculated. For alpha helix it is 100 degrees, for 3-10 helices it will
31       be smaller, for 5-helices it will be larger.
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33         3.  Rise per residue (file rise.xvg). The helical rise per residue is
34       plotted as the difference in Z-coordinate  between  Ca  atoms.  For  an
35       ideal helix this is 0.15 nm
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37         4.  Total  helix  length  (file len-ahx.xvg). The total length of the
38       helix in nm. This is simply the average rise (see above) times the num‐
39       ber of helical residues (see below).
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41        5. Number of helical residues (file n-ahx.xvg). The title says it all.
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43        6. Helix Dipole, backbone only (file dip-ahx.xvg).
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45         7.  RMS  deviation  from ideal helix, calculated for the Calpha atoms
46       only (file rms-ahx.xvg).
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48        8. Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).
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50        9. Average Phi and Psi angles (file phipsi.xvg).
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52        10. Ellipticity at 222 nm according to  Hirst and Brooks
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FILES

57       -s topol.tpr Input
58        Run input file: tpr tpb tpa
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60       -n index.ndx Input
61        Index file
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63       -f traj.xtc Input
64        Trajectory: xtc trr trj gro g96 pdb cpt
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66       -to gtraj.g87 Output, Opt.
67        Gromos-87 ASCII trajectory format
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69       -cz zconf.gro Output
70        Structure file: gro g96 pdb etc.
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72       -co waver.gro Output
73        Structure file: gro g96 pdb etc.
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OTHER OPTIONS

77       -[no]hno
78        Print help info and quit
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80       -[no]versionno
81        Print version info and quit
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83       -nice int 19
84        Set the nicelevel
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86       -b time 0
87        First frame (ps) to read from trajectory
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89       -e time 0
90        Last frame (ps) to read from trajectory
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92       -dt time 0
93        Only use frame when t MOD dt = first time (ps)
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95       -[no]wno
96        View output xvg, xpm, eps and pdb files
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98       -r0 int 1
99        The first residue number in the sequence
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101       -[no]qno
102        Check at every step which part of the sequence is helical
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104       -[no]Fyes
105        Toggle fit to a perfect helix
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107       -[no]dbno
108        Print debug info
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110       -prop enum RAD
111        Select property to  weight  eigenvectors  with.  WARNING  experimental
112       stuff:  RAD,  TWIST,  RISE,  LEN,  NHX,  DIP,  RMS,  CPHI,  RMSA,  PHI,
113       PSI,  HB3,  HB4,  HB5 or  CD222
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115       -[no]evno
116        Write a new 'trajectory' file for ED
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118       -ahxstart int 0
119        First residue in helix
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121       -ahxend int 0
122        Last residue in helix
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO