I am performing MD simulations for a protein complex after docking to check the stability of the complex. I am unsure which force field will best reflect whether the two proteins are binding well. Most papers use AMBER14SB and CHARMM36. Please explain the differences between these two force fields. Thank you for your assistance.
AMBER14SB is designed with a focus on accurately representing the dynamics and energetics of proteins and nucleic acids. It includes specific parameters for side-chain torsions and backbone dihedrals, optimized using a combination of quantum mechanical calculations and experimental data whereas CHARMM36 focuses on a balanced treatment of proteins, lipids, carbohydrates, and nucleic acids, aiming for broad applicability across biomolecular simulations.
AMBER14SB places a strong emphasis on optimizing torsion angles for proteins, whereas CHARMM36 aims for a broader applicability across various biomolecules.
So as per my opinion since you have to look for the protein complex you should go with AMBER
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