This is an example of how to use MDAnalysis to analyse protein trajectories - calculating things like RDF, coordination numbers, average angles, etc.
The main script here is analyse.py.
It defines a class Universe which works the same way as
MDAnalysis.Universe,
but with added functionality.
This script is meant to be used as like a module, i.e., it is meant to be imported in another script or interactive shell:
import analyse as ana
uni = ana.Universe(<topology_file>, <coordinate_file>, *args, **kwargs )
Now you have a Universe object
which inherits everything from MDAnalysis.Universe
and adds some extra functionality, like centering the protein,
getting angles and distances, etc.
One important feature implemented in analyse.Universe
is the function to center the protein within the box
and write it to a new file.
For example,
uni = ana.Univese('output.pdb', 'output.dcd')
uni.center_protein_write('centered_output.dcd')
will center the protein and save it to centered_output.dcd.
It is really important that you center the protein first, then load the new centered trajectory for further analysis. Otherwise, the distance based calculations (RDF, RMSD, etc) might not be right.
angles_distances.py
shows how to import analyse.py as a module
and calculate angles and distances of particular atom selections per frame.
This data is then plotted using matplotlib.
If importing analyse.py you really don't need anything else here, it is stand alone.
However, running it directly,
python analyse.py
will require at least the output.pdb and output.pdb,
unless they are changed within the script.
Running it directly will also plot and save some RDF, RMSD, and Coordination
figures, as done within the main function of analyse.py.
The following notebooks automate much of the analysis:
angles.ipynb
distances.ipynb
rdf.ipynb
To use the example notebooks, you will have to create the following files in exactly the location shown:
trajectories/input.pdb (original 1ZNF pdb file)
trajectories/MD-1ZNF/OPLS-AA/centered_output.dcd
trajectories/MD-1ZNF/opt-OPLS-AA/centered_output.dcd
trajectories/MD-1ZNF/CTPOL/centered_output.dcd
trajectories/MD-1ZNF/opt-CTPOL/centered_output.dcd
To plot CT vs time, make sure you have the file:
CT-data.dat
use the notebook:
ct_vs_time.ipynb