gmx-helix man page

gmx-helix ā€” Calculate basic properties of alpha helices

Synopsis

gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
          [-cz [<.gro/.g96/...>]] [-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:

Options

Options to specify input files:

-s [<.tpr>] (topol.tpr)

Portable xdr run input file

-n [<.ndx>] (index.ndx)

Index file

-f [<.xtc/.trr/...>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

Options to specify output files:

-cz [<.gro/.g96/...>] (zconf.gro)

Structure file: gro g96 pdb brk ent esp

Other options:

-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

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

Referenced By

gmx(1).

Sep 15, 2017 2016.4 GROMACS