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gmx-dyndom - Online in the Cloud

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This is the command gmx-dyndom 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-dyndom - Interpolate and extrapolate structure rotations

SYNOPSIS


gmx dyndom [-f [<.pdb>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]]
[-firstangle <real>] [-lastangle <real>] [-nframe <int>]
[-maxangle <real>] [-trans <real>] [-head <vector>]
[-tail <vector>]

DESCRIPTION


gmx dyndom reads a .pdb file output from DynDom (http://www.cmp.uea.ac.uk/dyndom/). It
reads the coordinates, the coordinates of the rotation axis, and an index file containing
the domains. Furthermore, it takes the first and last atom of the arrow file as command
line arguments (head and tail) and finally it takes the translation vector (given in
DynDom info file) and the angle of rotation (also as command line arguments). If the angle
determined by DynDom is given, one should be able to recover the second structure used for
generating the DynDom output. Because of limited numerical accuracy this should be
verified by computing an all-atom RMSD (using gmx confrms) rather than by file comparison
(using diff).

The purpose of this program is to interpolate and extrapolate the rotation as found by
DynDom. As a result unphysical structures with long or short bonds, or overlapping atoms
may be produced. Visual inspection, and energy minimization may be necessary to validate
the structure.

OPTIONS


Options to specify input files:

-f [<.pdb>] (dyndom.pdb)
Protein data bank file

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

Options to specify output files:

-o [<.xtc/.trr/...>] (rotated.xtc)
Trajectory: xtc trr gro g96 pdb tng

Other options:

-firstangle <real> (0)
Angle of rotation about rotation vector

-lastangle <real> (0)
Angle of rotation about rotation vector

-nframe <int> (11)
Number of steps on the pathway

-maxangle <real> (0)
DymDom dtermined angle of rotation about rotation vector

-trans <real> (0)
Translation (Angstrom) along rotation vector (see DynDom info file)

-head <vector> (0 0 0)
First atom of the arrow vector

-tail <vector> (0 0 0)
Last atom of the arrow vector

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