Supplementary Material: Molecular Dynamics Simulations of IgE, LNP, and PEG/PGL Systems

# Supplementary Material: Molecular Dynamics Simulations of IgE, LNP, and PEG/PGL Systems

This archive contains the input files, topologies, parameter files, and selected output files for the molecular dynamics simulations presented in the manuscript.

## Contents

- `ige_2wqr/` – Simulations of free IgE (PDB 2wqr).  
  - `new_2wqr/` – Essential dynamics data (RMSD, gyration, distances) and covariance analysis.  
- `ige_fceri_2y7q/` – Simulations of IgE bound to FcεRI (PDB 2y7q).  
  - `new_ige_fceri_2y7q/` – Essential dynamics data and advanced analysis (including covariance).  
- `omalizumab_7sht/` – Simulations of Omalizumab bound to IgE‑FcεRI (PDB 7sht).  
  - `new_omalizumabe_7sht/` – Essential dynamics data and covariance matrix analysis.  
- `peg_pgl_docking/` – Docking simulations of PEG and PGL with IgE.  
  - `main_docking/` – All main docking scripts, topologies, and output files.  
  - `mmpbsa_real_docking/` – MMPBSA analysis files.
- `lnp_simulations/` – Coarse‑grained Martini simulations of lipid nanoparticles (LNPs) with and without mRNA.

## File Types

- `.gro` – GROMACS coordinate files.  
- `.pdb` – Structure files.  
- `.top`, `.itp` – Topology and include files.  
- `.mdp` – Parameter files for energy minimization, equilibration, and production.  
- `.ndx` – Index files for analysis.  
- `.xvg` – Output data (energies, RMSD, etc.).  
- `.log` – Simulation logs.  
- `.edr`, `.cpt` – Energy and checkpoint files (small).  
- `.sh`, `.py` – Analysis and utility scripts.  
- `.json`, `.md`, `.txt` – Reports and metadata.  

Large trajectory files (`.trr`, `.xtc`) are **not** included due to size constraints but can be regenerated using the provided input files and the scripts from the associated Zenodo records (Karikó‑Scripts I & II).

## How to Reproduce

1. Install GROMACS 2022.3+ and the necessary force fields (Martini 3 for LNP simulations, CHARMM36/amber for atomistic simulations).  
2. For each system, enter its directory and follow the standard GROMACS workflow:  
gmx grompp -f minim.mdp -c system.gro -p system.top -o minim.tpr
gmx mdrun -deffnm minim
...

text
The exact `.mdp` files are provided in each subdirectory.  
3. For the LNP simulations, the Martini 3 force field must be downloaded separately (see `force_fields/` directory if included, or obtain from [cgmartini.nl](http://cgmartini.nl)).  
4. The docking simulations require the scripts from Karikó‑Scripts II.  

## Citation

If you use these data, please cite:

- The associated research article (when published).  
- The Zenodo records:  
- Karikó‑Scripts I: [10.5281/zenodo.18788715](https://doi.org/10.5281/zenodo.18788715)  
- Karikó‑Scripts II: [10.5281/zenodo.18790272](https://doi.org/10.5281/zenodo.18790272)  
- This supplementary material: *DOI to be assigned after upload*  

## License

Same as the script collections – CNRI Python Open Source GPL Compatible License.