This repository corresponds to the review article entititled Beyond benzamide-trypsin & alanine dipeptide: pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments It contains orer parameters as a part of Plumed files and other inputs necessary to perform further computational study.
Informations on the folder:
- WT-TIP3P: contains plumed.dat file and PCA eigenvector (ev1.dat) necessary to peform 1D PCA well-tempered metadynamics with Plumed 1.3.
- 2D-PCA: contains inputs to perform 2D PCA metadynamics with Plumed 2.5 or higher.
- Metadynamics-torsion: metadynamics with torsion CVs (chi1 and chi2 angles of Tyr)
- Metadynamics unbining: metadynamics simulation which using centre of mass CV to facilitate ligand unbining from plasmepsin-II.
- Metadynamics-COM: 2D metadynamics simulation using COM CVs described here https://www.biorxiv.org/content/10.1101/2020.04.27.062539v1
- Plumed-PasAg: plumed input which uses passive-agressive classifier
- Plumed-TICs: plumed input for TICA using dihedral angles.
- Plumed-reweight: reweighting script
- TICA-generation: scripts to perform TICA analyses on plasmepsin-II.
- plasmepsin-tica-tip4p-md.ipynb contains TICA generation using resid 69-91 (numbering according to .tpr file)
- variational-autoencoder: shows how to use variational autoencoder (MSM VDE) on the TICs. similar in spirit of using RAVE on SGOOP.
Softwares required:
- Plumed 1.3, 2.5
- Python 3.6 or higher
- MDtraj
- Gromacs patched with plumed
- SciPy for machine learning
- Gnuplot (plotting)
- Jupyter Notebook
- MSMBuilder
- Variational Dynamic Encoder (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398762/), Github: https://github.com/msmbuilder/vde
Please contact bhakatsoumendranath@gmail.com if you need more information.