SAMFF

Understanding 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