GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  GMX-HELIX (1)

NAME

gmx-helix - Calculate basic properties of alpha helices

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

gmx helix [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-f [<.xtc/.trr/...>]] [-cz [<.gro/.g96/...>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
[-r0 <int>] [-[no]q] [-[no]F] [-[no]db] [-[no]ev]
[-ahxstart <int>] [-ahxend <int>]

DESCRIPTION

gmx helix computes all kinds of helix properties. First, the peptide is checked to find the longest helical part, as 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 calculated 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 an alpha-helix it is 100 degrees, for 3-10 helices it will be smaller, and 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 Calpha 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. Helix dipole, backbone only (file dip-ahx.xvg). 6. RMS deviation from ideal helix, calculated for the Calpha atoms only (file rms-ahx.xvg). 7. Average Calpha - Calpha dihedral angle (file phi-ahx.xvg). 8. Average phi and psi angles (file phipsi.xvg). 9. Ellipticity at 222 nm according to Hirst and Brooks.

OPTIONS

Options to specify input and output files:

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa

-n [<.ndx>] (index.ndx) (Input)
Index file

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng

-cz [<.gro/.g96/...>] (zconf.gro) (Output)
Structure file: gro g96 pdb brk ent esp

Other options:

-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

-[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 GROMACS is available at <http://www.gromacs.org/>.

Search for    or go to Top of page |  Section 1 |  Main Index


VERSION 5.0.6 GMX-HELIX (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.