This is the command gmx-rama that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-rama - Compute Ramachandran plots
SYNOPSIS
gmx rama [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-o [<.xvg>]] [-b <time>]
[-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
DESCRIPTION
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 files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
Options to specify output files:
-o [<.xvg>] (rama.xvg)
xvgr/xmgr file
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
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
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