g_rama1
Compute ramachandran plots
Part of gmx-rama(1).
Usage
gmx rama
[-f
[<.xtc/.trr/ ...
>]]
[-s
[<.tpr/.tpb/ ...
>]]
[-o
[<.xvg>]]
[-nice
<int>]
[-b
<time>]
[-e
<time>]
[-dt
<time>]
[-
[no]
w]
[-xvg
<enum>]
Overview
gmx rama selects the phi/psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you can select out specific residues.
Options
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-o [<.xvg>] (rama.xvg) (Output)
xvgr/xmgr file
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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
Releases
5 releases since Debian 4.0 (Etch); the text changed 4 times.