Resources

Here you can find a collection of computational scripts and guides that I have developed during my research. These tools are designed to streamline common tasks in computational chemistry. Please feel free to use and modify them for your own work.

Computational Scripts

Gaussian IRC Log to XYZ Converter

The Problem: The first step in many post-processing workflows, including preparing for an EDA calculation, is to extract all the geometric structures from a Gaussian Intrinsic Reaction Coordinate (IRC) .log file into a simple, multi-structure .xyz file.

The Solution: This Python script automates the process. It reads one or more Gaussian IRC .log files, extracts the coordinates for every point along the reaction path, and writes them into a single, correctly ordered .xyz file. This .xyz file is the required input for the next script in this workflow.

How to Use:

  1. Prerequisites: Ensure you have Python3 installed. This script has no external library dependencies.
  2. Download the Script:
  3. Run from the Command Line: Open your terminal, navigate to the directory containing your .log file(s), and run the script: 
    python IRC2XYZ.py your_irc_file.log
  4. Output: The script will create a new file named your_irc_file.xyz in the same directory.

IRC-XYZ to EDA Input Generator for Solvated Systems

The Problem: Performing an Activation Strain Model (ASM) with Energy Decomposition Analysis (EDA) on a solvated system in the Amsterdam Modeling Suite (AMS) is not straightforward. The Fragments block required by PyFrag is often incompatible with the Solvation block, preventing direct calculation.

The Solution: This Python script provides a robust workaround. It takes the multi-structure .xyz file generated by the script above and creates a complete set of input folders for each point along the reaction coordinate. Each folder contains the necessary submission scripts (complex.sh, frag1.sh, frag2.sh) correctly formatted for a solvated EDA calculation.

How to Use:

  1. Prerequisites: Ensure you have Python3 and the following libraries installed:
    • RDKit: conda install -c conda-forge rdkit
    • xyz2mol: pip install xyz2mol
  2. Download the Script:
  3. Configure the Script: Open the IRC-XYZ2EDA.py file and modify the “USER CONFIGURATION SECTION” at the top to define the charge and atomic composition of your specific fragments.
  4. Run from the Command Line: 
    python IRC-XYZ2EDA.py your_irc_file.xyz
  5. Output: The script will create a series of numbered folders (e.g., IRC_point_1, IRC_point_2), each containing the three .sh files needed for the calculation.

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