CheckAdaptLig flow is a tool that helps the user to investigate an adaptive-like simulation (Adaptive or AdaptiveGoal). The flow will inspect the trajectory providing general information about the simulations and attempts to automatically build a Markov State Model (MSM). Furthermore, several analysis of the model are performed to provide useful information:
The flow summarizes all the information in HTML, which can be open and read with any web browser
Get the data for running the CheckAdaptLig flow examples here.
Analysis of a Adaptive Goal of D3-Receptor and Eticlopride
To analyze the example case, which uses D3 receptor as protein and Eticlopride as ligand, one can use the following command:
aceflow CheckAdaptLig --inputtrjs checkadaptlig/data --inputtopo checkadaptlig/Structures/structure.pdb --outdir test_checkadaptlig --metric distances
Finally, one can visualize the results by opening the HTML report using: