Processing Interaction dat files from Maestro

Post-process the output .dat file from Maestro (Schrodinger) after a molecular dynamics with Desmond.

This jupiter notebook shows the steps to process the "raw data" or .dat files from Mestro after molecular dynamics. Specifically, consider the following files:

• PL-Contacts_HBond.dat
• PL-Contacts_Hydrophobic.dat
• PL-Contacts_Ionic.dat
• PL-Contacts_Pi-Cation.dat
• PL-Contacts_Pi-Pi.dat
• PL-Contacts_WaterBridge.dat

1. Preparation

• Create a folder with the necessary files. For example:

mkdir InteractionAnalysis

mv PL-* InteractionAnalysis/

2. Processing

Download the jupyter notebook file on this folder "InteractionAnalysis" (previous step) . To run it you just need to open a console and type:

jupyter-notebook

Open the jupiter notebook file and execute the steps.

The output will be an excel file (called Interaction.xlsx) which you can plot with another program (e.g. Excel, GraphPad, plotly, R, etc). You can apply more lines of code to this notebook to plot as you like!

Additionally, an image of the plot will be saved in png format.

This is the Interaction.xlsx file

3. Example of plots

Example using Matplotlib

Other style using Matplotlib

Example using GraphPad

Note: The interaction file PL-Contacts_Metal is not processed in this version.