TFM

Contains all the codes used to perform the necessary simulations for the Master Final Work.

General Guidelines

Add a Protein

For all codes used in this work, if a protein different than WT and shuffle must be added, this are the steps to follow:

1. Open analyse.py and add your protein to the proteins DataFrame (if you want to generate new initial configurations for WESTPA, add your protein to analyse_ini.py too).
2. A new pickle from the new group of proteins will be generated if any of the analyse programs are used (or imported). If not, generate the new pickle in order to include the new protein. This can be done in example by running lines 48-51 on the analyse_ini.py and executing the cell.
3. If you want to use different parameters for the residues, add the corresponding residues.csv to the directory or modify the existing file by adding your data.

Contents

1. /INITIAL_CONFIG: Directory containning all the necessary files to generate the initial configurations of the system to use in the WESTPA enviorement.
2. /WESTPA: Directory containning all the necessary files and directories to perform a WESTPA simulation of peptide agregation.