Force field input files and tutorials
Parameters for the AMBER/GAFF force field
The Amber/GAFF suite of force fields is widely used by the molecular simulation community. We have recently developed Lennard-Jones parameters  that better describe ion-ion and ion-TIP3P water interactions, fully compatible with AMBER/GAFF. We provide improved parameters for the interaction of anions (carboxylates, sulfates, sulfonates, phosphates) with TIP3P water and with important cations (sodium, ammonium and primary amines). We strongly recommend using these parameters to adequately describe, e.g., salt bridges between acidic amino acids and lysine, and protein solvation at high NaCl concentrations. Many of the ions are present in buffer solutions typically used experimentally; our parameters enable investigating the impact of buffers on protein structure and dynamics.
To implement these parameters please follow the tutorial below. You can also email Ana Vila Verde for input files; if we have them, we will happily pass them to you.
"Modifying Lennard-Jones Parameters in the Amberff14SB force field."
In this tutorial you will learn to:
- Modify the self-interaction Lennard-Jones parameters of oxygens of carboxylate groups in proteins.
- Modify the Lennard-Jones parameters defining the interaction between sodium ions and the oxygens of carboxylate groups in proteins.