Probe-GridMap-Builder

🧪 Probe GridMap Builder

Probe GridMap Builder is a local web-based software interface designed to analyze molecular dynamics (MD) trajectories in trr/nc/xtc format, powered by the AMBER cpptraj backend. It enables users to generate grid-based interaction maps between protein structures and solvent probe atoms across dynamic frames. The runtime environment package is freely available here. The Probe GridMap Builder software package is freely available here. 👉 Live Demo

✅ Features

• Upload .trr or .nc trajectory files
• Grid map generation via cpptraj
• Cluster analysis and PDB annotation via cluster.py
• Automatic packaging of results (PDB + summary)

📦 Conda Environment Setup

# 1. Extract GridMap_denv.tar.gz 
tar -xzf GridMap_env.tar.gz

# 2. Activate Environment
source GridMap_env/bin/activate

🚀 Run the Server

python probe-gridmap.py

open the http://127.0.0.1:8086

📝 Usage

1. Upload your .trr or .nc trajectory file via the web interface.
2. Upload the corresponding .pdb file and choose probe atoms.
3. Submit the job, and download the result ZIP containing: • nonortho.pdb • nonortho_mark.pdb • cluster_summary.txt