Molecular dynamics analysis (ANATRA)
Introduction.
Graphical trajectory analysis
Make a trajectory movie (TRAGRA)
Dispaly a trajectory (TRAGRL)
Make a centered trajectory movie (TRACEN)
Follow atoms through a trajectory (FOLLOW)
Make a trajectory movie (TRASPH)
Movie of hydrogen bonds in sphere (TRAHBO)
Follow one atom through trajectory (TRA1AT)
Looping automatically through a movie (LOOPER)
Activating atoms
Activate all atoms (USEALL)
Activate all alpha carbons (USECA)
Parameters (PARAMS)
Pickability flag (PCWHAT)
Numerical trajectory analysis
Initializing the setup of the anatra menu (WADINI)
Initializing the script (WADISC)
WADSSC (shoing the script)
Run the script (WADEXE)
Evaluate the results of a previous run of the script (WADANA)
Using DSSP to evaluate geometrical properties (WADSSP)
Following the secondary structure as a function of time (WADHST)
Following a inter atomic distance through time (WADDIS)
Following an angle through time (WADANG)
Following a torsion angle through time (WADTRS)
Following a hydrogen bond through time (WAD1HB)
Following a phi/psi angle through time (WAD1PP)
Following the radius of gyration as a function of time (WADGYR)
Following backbone-backbone hydrogen bonds as a function of time (WADHBO)
Following dihedral angles as a function of time (WADDIH)
Following solvent accessible surface as a function of time (WADACC)
Calculating the RMS of positional fluctuations (WADFLC)
Isolating one frame out of a trajectory (WADGRO)
Do most of the fast-to-check overall analyses (WADALL)
Other options
Change the project number (PROJEC)
Count the frames in a trajectory (TRACNT)
Analyse one distance through a trajectory (ANADST)
Analyse atomic volume through a trajectory (ANAVOL)
Analyse one hydrogen bond through a trajectory (ANAHBO)
Look at mobility in a trajectory (TRARMS)
Run a WHAT IF script over a trajectory (TRASCR)
Avoid across box atomic bonds (BNDCHK)