cAMP Binding to GmCNGC30 Activates Channel Activity

Overview

This project simulates the binding of cAMP to GmCNGC30 and its effect on channel activation.
The workflow performs template-based docking, linker conformer selection, and energy minimization using AmberTools.
All results are automatically saved in the result/ folder.

The key steps of this project—structure preparation, force-field parameter generation, and energy minimization—all rely on AmberTools 23. For installation instructions and usage guidelines for AmberTools, please refer to the official documentation: https://ambermd.org/AmberTools.php

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Directory Structure

The repository is organized as follows:

project_root/
├── environment.yml        # Conda environment configuration
├── code/                  # Source code and execution scripts
│   ├── run.sh             # Main execution script
│   └── ...
├── data/                  # Input data and intermediate files
│   └── ...
├── result/                # Output directory for final results
└── README.md

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Environment Setup

Make sure you have Conda installed.

You can configure the entire environment for this project — including AmberTools 23 and all other dependencies — by running the following commands:

conda env create -f environment.yml
conda activate AmberTools23

Usage

To run the template-based docking, linker conformer selection, and energy minimization pipeline, simply execute the main workflow script. This script performs all steps automatically, including preparing input files, running AmberTools modules, and saving results to the result/ directory.

cd code
bash run.sh

After the script finishes:

• All intermediate files will be stored in the data/ folder.

• Final minimized complexes and docking outputs will appear in the result/ folder.