Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

This repo provides all details to repertory and validate the paper Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems (doi: https://doi.org/10.1101/2020.04.27.062539)

1. Preparation folder contains topology, .mdp and .gro file to generate .tpr files to perform simulation with TIP4P-Ew water model
2. TIP3P-MD1 and MD2 contains plumed.dat files to monitor and .tpr files to run MD simulations. MD1 and MD2 denotes MD simulations starting with different initial starting velocities.
3. Torsion TIP3P and TIP4P contains plumed.dat file which uses torsion angles as CVs (as described in the paper) to perform metadynamics simulations.
4. PCA-TIP3P contains plumed.dat file which uses PC1 and PC2 as CVs to perform metadynamics simulations (see the paper for analyses and plots)
5. COM TIP3P and TIP4P contains plumed.dat files to perform metadynamics simulations with centre of mass CVs (see full description in our paper).

Snapshots from clustering (using K-centers algorithm installed within Enspara) can be accessed here: https://www.dropbox.com/sh/xikqkkeiqajk9eu/AAAae-IkivyVXaqIbaloaLwqa?dl=0 The clustering was performed (using the build_msm.py script which can be accessed inside Clustering-script) on apo Plm-II using one of the MD trajectory with TIP3P water model.