Pelissimo

This repository contains certain python scripts to analyze PELE simulations: analyze. Some others are meant to automatize specific PELE simulations in different ways: protocol.

Contents

• 1. analysis: Directory with the code related to analyze PELE simulations:

  • 1.1. disc.py: Script to: (1) Read all the information about a metric in a simulation and calculating different scoring functions. (2) Make plots of the evolution of the Boltzmann weighted average or minimum of a certain metric throughout a simulation.

  • 1.2. analysis.py: Script to analyze simulations.

  • 1.3. pele_fetcher.py: Script that fetches specific snapshot of a simulation.

  • 1.4. rmsd.py: Script that prepares all to run an rmsd calculation in MN4.

  • 1.5. qm.py: Script to optimize ligand, calculate charges and prepare ligand to put results in a folder ready to make peleffy parametrize the ligand.

• 2. protocol: Directory with code related to the pelissimo protocol that is being assembled.

  • 2.1 corrector: Directory containing the code involved in the correction of the energies of a simulation.

    • 2.1.1 correction.py: Script that retrieves entropy and strain corrections and implements them in the reports of the induced fit simulation.

  • 2.2 entropy: Directory with the code related to the Ligand Conformational Entropy (LiCE) calculation

    • 2.2.1 lice.py: Script that reads the results from dihedral clustering and further processes information to obtain an entropy change.

    • 2.2.2 dihedral_clustering.py: Script that calculates dihedral angles for all the rotatable bonds in all the conformations reached by the ligand in a simulation. This information will be used to cluster conformations.

    • 2.2.2 propy.py: Script that calculates dihedral angles for all peptidic bonds phi and psi of the backbone in all the conformations reached by the ligand in a simulation. This information will be used to cluster conformations.

    • 2.2.4 entropy.py: Script that ensembles the other three to make a complete entropy analysis of a simulation.

  • 2.3 initial_files: Directory with an example of the necessary files to perform a full simulation of the protocol.

  • 2.4 strain: Directory with the code related to the calculation of the Ligand Internal Energy (LInEn).

    • 2.4.1. ligand.py: Script to calculate strain and entropy with a PELE simulation of the ligand.

Examples

In all cases the usage of the flag -h is recommended in order to understand the possibilities offered by the script.

python path/to/code/analysis.py -h

In case of doubt the code can be read since all the functions are commented and explained.

analysis

All the analysis scripts are designed to be run from the father directory of the output directory generated by PELE.

1. disc.py: In this case we want to analyze the reports inside output_1 and we want to take a look at the fifth metric in the reports.

   python path/to/code/disc.py -d ouput_1 -c 5

2. analysis.py: If we want to make 50 bootstrap datasets from the results in output_2 regarding the sasa:

python path/to/code/analysis.py -d ouput_2 -ns 50 -m sasa --bootstrap

If we want to select the snapshots the first quantile of the BindingEnergy and analyze the energetic results of the BindingEnergy:

python path/to/code/analysis.py -rn rmsd_report -es 3 -q ['BindingEnergy',0.25] --filter --analyze -m BindingEnergy

3. pelefetcher.py: If we want to extract the pose in epoch 4, trajectory 33, model 7 and save it as 1MTS_min.pdb:

python path/to/code/pele_fetcher.py -e 4 -t 33 -m 7 -s 1MTS_min

4. rmsd.py: We will require the ligand structure that we will base our RMSD upon (i.e. 1HPV_lig.pdb). :

python path/to/code/rmsd.py -pdbr 1HPV_lig.pdb

protocol

entropy

1. dihedralclustering.py: If we want to calculates the 1A28's ligand dihedrals of all the simulation stored in the folder called output_original and cluster them with bins:

python path/to/code/dihedral_clustering.py -f 1A28_lig.pdb -d output_original 

strain

1. linen.py: This code requires a DataLocal folder of the ligand. If we want to make a ligand-alone simulation of the 1A28_lig.pdb file with OpenFF and OBC as forcefield and solvent model:

python path/to/code/linen.py -f 1A28_lig.pdb -ff OpenFF-OPLS2005 -sm OBC