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GateWizard Documentation

Welcome to GateWizard, a tool for membrane protein preparation and molecular dynamics analysis.

Overview

GateWizard is a Python-based GUI application designed to prepare protein membrane structures for molecular dynamics simulations. It integrates various computational tools to provide a unified interface for structure preparation, analysis, and plot customization.

Key Features

  • Protein Structure Preparation: Clean PDB files, and add missing atoms.
  • Propka Integration: Automatic pKa calculations with protonation state assignment
  • Protein Capping: Add ACE/NME caps to protein termini for proper MD simulations
  • Force Field Support: Compatible with Amber force fields (ff14SB, ff19SB, etc.)
  • Membrane System Building: Automated membrane protein insertion and equilibration protocols
  • Trajectory Analysis: RMSD, RMSF, distances, and radius of gyration calculations
  • Energy Analysis: NAMD log file parsing and visualization
  • Modern GUI: Built with CustomTkinter for an intuitive, cross-platform user experience

Quick Start

Installation

# Create conda environment with dependencies
conda create -n gatewizard -c conda-forge python sqlite ambertools=24 parmed=4.3.0 -y

# Activate environment
conda activate gatewizard

# Install GateWizard from PyPI
pip install gatewizard

Launch

gatewizard

Upgrade

pip install --upgrade gatewizard

For more detailed installation instructions, see the Installation Guide.

Documentation Sections

System Requirements

  • Operating System: Linux, macOS, or Windows (with WSL recommended)
  • Python: 3.8 or higher
  • Conda: For managing dependencies (Miniconda or Anaconda)
  • RAM: Minimum 4GB (8GB+ recommended for large systems)
  • Disk Space: ~2GB for installation plus space for your projects

Getting Help

If you encounter issues or have questions:

  1. Check the Troubleshooting Guide
  2. Review the User Guide for usage instructions
  3. Submit an issue on GitHub (if repository is public)

Contributing

GateWizard is open-source software. Contributions are welcome! See our development guidelines for more information.

License

GateWizard is licensed under the MIT License.

Copyright (c) 2025 Constanza González and Mauricio Bedoya

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Authors

  • Constanza González
  • Mauricio Bedoya

Citation

If you use GateWizard in your research, please cite:

[Citation information to be added]

Last updated: January 2026