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AutoDock tools
Leif Laaksonen CSC 2001
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This is the main widget for the AutoDock trajectory display and analysis facility.

There are first 4 file readers:

With an AutoDock trajectory I mean the "ligand.tout" file as in the following:

The traj command which is used in the trajectory output, creates trajectories in two formats, one in PDB format which is written to the log file specified by the -l flag, and one in a raw ASCII format which is written to the standard output. For example, if the command issued was:

autodock -p ligand.dpf -l ligand.trj.conv.log -c < trj.conv.com > ligand.tout

the file ligand.trj.conv.log will contain a PDB formatted list of all the trajectory steps, while the ligand.tout file will contain raw ASCII data, with one row for each atom in the ligand, and each column containing data. The command file trj.conv.com contains only the commands:

traj ligand.trj
stop

This was taken from Web pages and manuals at:
http://www.scripps.edu/pub/olson-web/doc/autodock/

gOpenMol is again calling this .tout file a .trj file but it should not be mixed with the original .trj file. A bit confusing I agree! To read and display a trajectory from the AutoDock do the following:

  1. First define the file name of the ligand either by directly writing the file and or by using the file browser. Then press the "Import" button to apply the file. It is possible to read several conformations of the ligand by clicking the "Append structure".
  2. If you also want to include the system (into which the ligand is docked) do the same as in the previous section but for the system.
  3. Last but not least define the trajectory file. Use the same approach as in the previous sections. Remember to press the "Import" button.

After this you should be able to see the number of frames displayed.

By default the display goes from the first frame to the last with the step 1. This can be changed by supplying new values in the respective fields.

It is possible to display the trajectory in a loop, one frame at the the backwards and forwards or go to the first and last frames.

Frame control:

There are two trajectory retrieval methods available:

    The fast method uses a pre-calculated index (jump) vector into the trajectory file for the various frames. This method is capable of retrieving a frame at a speed independent of the frame position in the file. However, be careful with this if you move files between Unix and Windows systems! The slow method is a "stupid" read process that always reads all the frames up to the needed frame. This process becomes very slow for big files but it is not sensitive to the characters at the end of the line.

At the bottom of the widget there is also a file writer to write out the ligand and system coordinates as *.pdbq files. This is very handy in case you import the atom partial charges and want to write a *.pdbq file with the new charges.

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LUL/2001
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