Conformational Sampling: cluster analysis

Introduction

Cluster analysis applied to multimol2 files resulting from a conformational sampling.

The procedure uses a combination of PyEMMA and OpenEye (OE Toolkit) Python tools.

Pre-requisite

Anaconda Python distribution

PyEMMA

OE Toolkit

Torsion angles list

File - Open - Choose the file (generally a mol2 file)

In the Conformational search window select the different panels clicking on the label on the bottom to setup the simulation:

• Conformational search panel
• Set the torsion angles
• Edit torsion - Edit - Add torsion - Flexible
• Click on save from the Selection tool panel

Check the file with the list of flexible torsion angles.

In the list of torsional angles obtained with Vega there is the atom name of the four atoms that define each flexible torsional angle. In the next steps the serial number of the atoms involved in each flexible torsion angles is required thus it is necessary to extract the information manually or with the help of Excel (to do: probably it is possible to extract the serial number of atoms involved in flexible torsion angles using the OE toolkits)

Analyses of the trajectory

Run Anaconda

Then, run Jupyter Notebook

In the Notebook file manager, move to the working directory

Put the file ClusterAnalysisFull.ipynb in the working directory and click on it from the Notebook file manager.

A new ipykernel is opened in the browser with all the Python instructions

• Change the name of the files according to the system under analysis