DownloadUnderstanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the adsorption orientation
of lysozyme on CH3-SAM.
For details, please refer to our publication:
Bhadra and Siu, "A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14
and GAFF" (submitted)
https://cbbio.online/software/SAMFF/index.html
Features
- Self-Assembled Monolayers
- Protein
- Force field
- Molecular Dynamics
- Parameterization
Project Samples
