1 .TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_helix - calculates basic properties of alpha helices
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-s" " topol.tpr "
9 .BI "\-n" " index.ndx "
10 .BI "\-f" " traj.xtc "
11 .BI "\-to" " gtraj.g87 "
12 .BI "\-cz" " zconf.gro "
13 .BI "\-co" " waver.gro "
15 .BI "\-[no]version" ""
27 .BI "\-ahxstart" " int "
28 .BI "\-ahxend" " int "
30 \&\fB g_helix\fR computes all kinds of helix properties. First, the peptide
31 \&is checked to find the longest helical part, as determined by
32 \&hydrogen bonds and phi/psi angles.
34 \&to an ideal helix around the \fI z\fR\-axis and centered around the origin.
35 \&Then the following properties are computed:
38 \&\fB 1.\fR Helix radius (file \fB radius.xvg\fR). This is merely the
39 \&RMS deviation in two dimensions for all Calpha atoms.
40 \&it is calced as sqrt((SUM i(x2(i)+y2(i)))/N), where N is the number
41 \&of backbone atoms. For an ideal helix the radius is 0.23 nm
43 \&\fB 2.\fR Twist (file \fB twist.xvg\fR). The average helical angle per
44 \&residue is calculated. For an alpha\-helix it is 100 degrees,
45 \&for 3\-10 helices it will be smaller, and
46 \&for 5\-helices it will be larger.
48 \&\fB 3.\fR Rise per residue (file \fB rise.xvg\fR). The helical rise per
49 \&residue is plotted as the difference in \fI z\fR\-coordinate between Calpha
50 \&atoms. For an ideal helix, this is 0.15 nm
52 \&\fB 4.\fR Total helix length (file \fB len\-ahx.xvg\fR). The total length
54 \&helix in nm. This is simply the average rise (see above) times the
55 \&number of helical residues (see below).
57 \&\fB 5.\fR Number of helical residues (file \fB n\-ahx.xvg\fR). The title says
60 \&\fB 6.\fR Helix dipole, backbone only (file \fB dip\-ahx.xvg\fR).
62 \&\fB 7.\fR RMS deviation from ideal helix, calculated for the Calpha
63 \&atoms only (file \fB rms\-ahx.xvg\fR).
65 \&\fB 8.\fR Average Calpha \- Calpha dihedral angle (file \fB phi\-ahx.xvg\fR).
67 \&\fB 9.\fR Average phi and psi angles (file \fB phipsi.xvg\fR).
69 \&\fB 10.\fR Ellipticity at 222 nm according to Hirst and Brooks.
74 .BI "\-s" " topol.tpr"
76 Run input file: tpr tpb tpa
78 .BI "\-n" " index.ndx"
84 Trajectory: xtc trr trj gro g96 pdb cpt
86 .BI "\-to" " gtraj.g87"
88 Gromos\-87 ASCII trajectory format
90 .BI "\-cz" " zconf.gro"
92 Structure file: gro g96 pdb etc.
94 .BI "\-co" " waver.gro"
96 Structure file: gro g96 pdb etc.
100 Print help info and quit
102 .BI "\-[no]version" "no "
103 Print version info and quit
105 .BI "\-nice" " int" " 19"
108 .BI "\-b" " time" " 0 "
109 First frame (ps) to read from trajectory
111 .BI "\-e" " time" " 0 "
112 Last frame (ps) to read from trajectory
114 .BI "\-dt" " time" " 0 "
115 Only use frame when t MOD dt = first time (ps)
118 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
120 .BI "\-r0" " int" " 1"
121 The first residue number in the sequence
124 Check at every step which part of the sequence is helical
127 Toggle fit to a perfect helix
132 .BI "\-prop" " enum" " RAD"
133 Select property to weight eigenvectors with. WARNING experimental stuff: \fB RAD\fR, \fB TWIST\fR, \fB RISE\fR, \fB LEN\fR, \fB NHX\fR, \fB DIP\fR, \fB RMS\fR, \fB CPHI\fR, \fB RMSA\fR, \fB PHI\fR, \fB PSI\fR, \fB HB3\fR, \fB HB4\fR, \fB HB5\fR or \fB CD222\fR
136 Write a new 'trajectory' file for ED
138 .BI "\-ahxstart" " int" " 0"
139 First residue in helix
141 .BI "\-ahxend" " int" " 0"
142 Last residue in helix
147 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.