Trajectories can also be read into AVS using the read field module. The trajectory file is essentially a set of "stacked" or concatenated PDB frames, and must be read in as a two dimensional field (being the number of atoms in the ligand, and the number of frames in the trajectory file). By paging through this field, using the orthogonal slicer , continuous replay of the trajectory can be achieved using an animate integer module to control which PDBQ frame is selected by the orthogonal slicer. This animates the sequence of sampled states and allows the user to view in real time the progress of the docking simulation.
Unlike AVS,
gOpenMol
is free, and can be dowloaded via the web from:
http://laaksonen.csc.fi/gopenmol/gopenmol.html
It has various
AutoDock
tools, including the ability to read in and view AutDock trajectories: see:
http://laaksonen.csc.fi/gopenmol/help/main_autodock_widget.html