MD-protocol

System building protocol for GPCRmd

The protocol is written in Python 3 programming language inside the Jupyter notebook file protocol_jupyter_notebook.ipynb.

Requirements

• Python 3
• STAMP software 4.4+ (Structural Alignment of Multiple Proteins).
• Visual Molecular Dynamics 1.9.3+ from University of Illinois (should be added to your PATH environment variable).
• Numpy 1.12.1+ for Python 3.
• HTMD 1.13.10+ from Acellera Ltd. form Python 3. You can obtain it here.
• Jupyter (core 4.4+) for Python 3 to open the python notebook.
• ACEMD from Acellera Ltd. and SLURM Workload Manager for running the molecular dynamics simulations.