kumaranu / drugdiscmdconformers

A python package to generate conformers for small molecules using molecular dynamics.

DrugDiscMDConformers

DrugDiscMDConformers is a package designed to generate molecular conformers using SMILES for drug discovery applications.

Outline of the Program

Main Script:

• make.bash

Supplementary Scripts:

1. main.py
2. confgen_rdkit.py
3. call_slurm.tcsh
4. run.py
5. sol_run.py
6. getEnergy.py
7. getEnergy_sol.py

Files and Directories Needed from the User:

1. run.slurm
2. sol_run.slurm

Summary of the Program

The package comprises several scripts, each with a specific purpose, aimed at facilitating the generation of molecular conformers and subsequent energy calculations. Here's a brief overview:

1. Main Script Execution:

   • The bash script main.bash invokes main.py, which retrieves the PDB structure for the protein and extracts the ligand.
   • main.py utilizes the confgen function from confgen_rdkit.py to generate conformers using rdkit.

2. Conformer Generation:

   • Conformers are segregated into different xyz inputs and stored in distinct directories, such as molecular_files/rdkit_conformer/.

3. Energy Calculations:

   • Energy calculations, for both solvated and non-solvated conformers, are submitted batchwise using call_slurm.tcsh.
   • Python scripts getEnergy.py and getEnergy_sol.py are employed to extract energies and sort conformations based on their energy.

4. Bound Ligand Conformation:

   • Energy calculations for the bound conformation of the ligand are also submitted.

5. CREST Calculations:

   • CREST calculations are independently submitted inside the molecular_files directory.

This package streamlines the process of molecular conformer generation and energy calculations, providing a comprehensive toolkit for drug discovery endeavors.

License

This project is licensed under the MIT License.

Author

Anup Kumar