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g_helix_d

NAME

g_helix - calculates everything you want to know about helices

SYNOPSIS

g_helix -s topol.tpr -n index.ndx -f traj.xtc -to gtraj.g87 -cz zconf.gro -co waver.gro -[no]h -nice int -b time -e time -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop enum -[no]ev -ahxstart int -ahxend int

DESCRIPTION

g_helix computes all kind of helix properties. First, the peptide is checked to find the longest helical part. This is 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:

1. Helix radius (file radius.xvg). This is merely the RMS deviation in two dimensions for all Calpha atoms. it is calced as sqrt((SUM i(x2(i)+y2(i)))/N), where N is the number of backbone atoms. For an ideal helix the radius is 0.23 nm

2. Twist (file twist.xvg). The average helical angle per residue is calculated. For alpha helix it is 100 degrees, for 3-10 helices it will be smaller, for 5-helices it will be larger.

3. Rise per residue (file rise.xvg). The helical rise per residue is plotted as the difference in Z-coordinate between Ca atoms. For an ideal helix this is 0.15 nm

4. 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).

5. Number of helical residues (file n-ahx.xvg). The title says it all.

6. Helix Dipole, backbone only (file dip-ahx.xvg).

7. RMS deviation from ideal helix, calculated for the Calpha atoms only (file rms-ahx.xvg).

8. Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).

9. Average Phi and Psi angles (file phipsi.xvg).

10. Ellipticity at 222 nm according to Hirst and Brooks

FILES

-s topol.tpr Input
 Generic run input: tpr tpb tpa xml 

-n index.ndx Input
 Index file 

-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb 

-to gtraj.g87 Output, Opt.
 Gromos-87 ASCII trajectory format 

-cz zconf.gro Output
 Generic structure: gro g96 pdb xml 

-co waver.gro Output
 Generic structure: gro g96 pdb xml 

OTHER OPTIONS

-[no]h no
 Print help info and quit

-nice int 19
 Set the nicelevel

-b time 0
 First frame (ps) to read from trajectory

-e time 0
 Last frame (ps) to read from trajectory

-dt time 0
 Only use frame when t MOD dt = first time (ps)

-[no]w no
 View output xvg, xpm, eps and pdb files

-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

-prop enum RAD
 Select property to weight eigenvectors with. WARNING experimental stuff:  RAD , TWIST , RISE , LEN , NHX , DIP , RMS , CPHI , RMSA , PHI , PSI , HB3 , HB4 , HB5 or CD222

-[no]ev no
 Write a new 'trajectory' file for ED

-ahxstart int 0
 First residue in helix

-ahxend int 0
 Last residue in helix

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.