Automatic Protocol for Ab-Initio-Interaction-Map

Overview

This project provides an automated protocol for generating Ab-Initio Interaction Maps (AIIM) using Python and Shell scripting. By following this protocol, users can efficiently compute a 3D interaction map between two molecules from their XYZ coordinates, which is crucial for identifying the sites where the molecules are most likely to interact with each other. The figure represents the stepwise workflow for generating an AIIM map for BODIPY and TPAB molecules. The blue regions on the van der Waals surface of BODIPY indicate where the TPAB molecule is most likely to interact with BODIPY. By following this protocol, one can generate AIIM maps for any two molecules.

The process involves several steps, including setting up a virtual environment, installing necessary dependencies, running the main script to generate a solvent box, equilibration and initial configuration, geometry optimization, and AIIM generation via convolution. These steps are designed to streamline the workflow and provide a comprehensive solution for AIIM generation.

Authors

Mohammad Pabel Kabir, Fang Liu

Requirements

AMBER16 or above

Packmol (https://m3g.github.io/packmol/)

pyvdwsurface module

Installation of Requirements

Step 1: Create a Virtual Environment

Install virtualenv if you don't have it: python2.7 -m pip install virtualenv

Create a virtual environment: python2.7 -m virtualenv vdw_surface

Activate the virtual environment: source vdw_surface/bin/activate

Step 2: Download and Install pyvdwsurface

Install Cython: python -m pip install cython

Clone the pyvdwsurface repository (optional: you can clone it in any folder): git clone https://github.com/rmcgibbo/pyvdwsurface.git

cd vdw_surface

cd pyvdwsurface

Install pyvdwsurface: python -m pip install .

Workflow Description

Step 1: Parameter File Generation for Individual Systems

Prepare a starting coordinates file (pdb or xyz) for the molecules for which you would like to generate an AIIM. Use antechamber to create AMBER parameters for the two systems and the solvent. Here, we use the example of BODIPY (system1) and TPAB (system2) molecules in ACN solvent:

antechamber -i system1.pdb -fi pdb -o system1.mol2 -fo mol2 -c bcc -s 2

antechamber -i system2.pdb -fi pdb -o system2.mol2 -fo mol2 -c bcc -s 2

antechamber -i solvent.pdb -fi pdb -o solvent.mol2 -fo mol2 -c bcc -s 2

Convert the resulting mol2 into an AMBER library file: tleap -f convert.leap

After this, you should have the following files: solvent.frcmod, solvent.prep, solvent.pdb, system1.lib, system1.frcmod, system1.pdb, system2.lib, system2.frcmod, system2.pdb

Note: Since both BODIPY and TPAB molecules contain a boron (B) atom, and the parameter for the B atom is not available in the Gaff force field, force field fitting is required. For our case, we did force field fitting to generate the parameter files.

Step 2: Solvent Box and Parameter Generation for the Whole System

Generate solvent box coordinates using the packmol.py script, which employs Packmol to place system1 and system2 in the solvent and creates a solvated.pdb file:

python 1.packmol.py

Generate parameter file for the whole system with the tleap.sh script, which uses tleap tools, loads parameter files for individual systems and generate parameter file for the whole system:

tleap -f 2.tleap.sh

This will generate system.pdb, system.parm, and system.rst files

Step 3: Minimization, Heating and Equilibration

Perform system minimization, heating, and equilibration for 100ps.

python 3.amber_input.py

Step 4: Initial Configuration Generation and Geometry Optimization

Take snapshots every 1ps from the equilibration trajectory file. The snapshots will be used as guess structrues for ab-initio geometry optimization.

python 4.guess_structrue_optimization.py

Step 5: Desity Calculation and Normalization

Calculate center of mass (COM) points of system2 molecule from the optimized geometry, calculate density of the COM points and Normalize.

python 5.make_pdb_from_opt.py

bash 6.align_BDP.sh

python 7.pdb_to_xyz.py

bash 8.vdw_surface.sh

Step 6: Generation of .mol2 File and AIIM

Generate mol2 file, which can be opened with a visualization software like VMD.

python 9.generate_mol2.py

Getting Started

To begin using this workflow, clone the repository and navigate to the root directory. Ensure that all required Python libraries (NumPy, Cython, pyvdwsurface, etc.) are installed. Follow the steps outlined in the README files within each directory to execute the workflow successfully.

Contributions

Contributions to this workflow are welcome. If you have suggestions for improvement or encounter any issues, please feel free to open an issue or submit a pull request.

License

This project is licensed under the MIT License. See the LICENSE file for more details.