Some miscellaneous scripts I made to do protein analysis using pytraj
This is a work in progress...
You can find the scripts I use in the scripts folder.
Loads the MD production files ready for processing. Before calculating any quantity it centers the molecule at the origin and minimizes RMSD.
Simple script to get PDB file from RCSB Protein Data Bank.
Runs afterProd.in using cpptraj, organizes data in folders as it's convenient for cppy.py
Removes water molecules for later analysis. The most important stuff is done with pytraj when running cppy.py.
Update PDB codes on codes_n_temps.csv according to the simulation data that it finds on the folders (which is outdated in this repository...).