General¶

Activating the virtual environment¶

If the installation recommendations on the previous page were followed, you would have set up a virtual Python environment for MD-TASK. If that is so, it is important that the environment be active whenever you use MD-TASK. To activate the environment, run the following command in the root MD-TASK folder (if that is where the environment was installed):

. venv/bin/activate

You will now have all the installed dependencies available and MD-TASK should work perfectly.

Add MD-TASK to your PATH¶

To make tools in the MD-TASK suite available from anywhere on the command line, add the root MD-TASK directory to your PATH environment variable as follows:

export PATH=/path/to/MD-TASK:$PATH

Trajectory vs Topology¶

Most of the MD-TASK tools require both a trajectory file and topology/structure file as input. This is because most trajectory formats only contain the atom co-ordinates and not the topological information such as atom and residue names, chains, and bond information. The topology file can be the PDB file that was used in the molecular dynamics simulation to produce the trajectory. When supplying these files, it is important to note that the trajectory file and topology file must contain the exact same number of atoms i.e. if the trajectory has been reduced to CA and CB atoms only (as described below), the topology file must be reduced to the same.

Reducing your trajectory¶

Molecular dynamics trajectories can be extremely large. However, MD-TASK tools only require the alpha and beta carbon atoms to be present. To save space and improve performance, the following VMD script can be used to reduce a trajectory, to the bare essentials:

mol load pdb example.pdb
set s1 [atomselect top "name CA or name CB and not solvent"]
animate write pdb example_small.pdb sel $s1
animate read xtc example.xtc waitfor all
animate write dcd example_small.dcd waitfor all sel $s1
quit

The above assumes that your topology file is a PDB file named example.pdb and that your trajectory is named example.xtc. It then writes out the reduced structure and trajectory to example_small.pdb and example_small.dcd respectively. You should change these names accordingly. You will also note that the above converts the trajectory from XTC to DCD format. This is not necessary, but has been added as an example for those who may want to do it.

For very large trajectories that do not fit in memory, reducing as shown above is necessary. Note that when reducing the trajectory, it is important that the same reduction should be applied to the topology PDB file i.e. the trajectory and topology files should have the exact same number of atoms. Failing to do this will result in an error.

Test Data¶

There is test data located in the ‘examples’ directory. Four files are included here:

File	Description
`wt.dcd`	An example trajectory that has been reduced to alpha and beta carbons only (used in the network analysis section)
`wt.pdb`	A PDB file that corresponds to the above trajectory - to be used for topology information (used in the network analysis section)
`mutant.dcd`	A mutated version of the above trajectory (used in the network analysis section)
`mutant.pdb`	A mutated version of the above topology file (used in the network analysis section)
`example_small.dcd`	An example trajectory that has been reduced to alpha and beta carbons only (used in the PRS section)
`example_small.pdb`	A PDB file that corresponds to the above trajectory - to be used for topology information (used in the PRS section)
`initial.xyz`	An XYZ co-ordinate file representing the initial conformation of a protein (used for PRS)
`final.xyz`	An XYZ co-ordinate file representing the target conformation of a protein (used for PRS)

Logging¶

All scripts in the suite have two arguments for logging. By default, logging is switched on and is written to the terminal. This can be changed with the following arguments:

Input	Flag	Description
Log file	`--log-file`	Provide a path to a file that will store the logging output of the command. By default, the output will be written to the terminal.
Silent	`--silent`	Switch off logging