Biological Forcefields

Amber

• https://ambermd.org/AmberModels.php

Proteins

• ff19SB + OPC: J Chem Theory Comput 2019;16:528
• ff14SB / ff99SB + TIP3P: J Chem Theory Comput 2015;11:3696

Nucleic Acids

• chiOL3: J. Chem. Theory Comput. 2011, 7, 2886

General Organic Ligands

• GAFF: J. Comput. Chem. 2004, 25, 1157
• Antechamber: J Mol Graph Model 2006, 25, 247. Automatic forcefield generator.

CHARMM

• https://mackerell.umaryland.edu/charmm_ff.shtml

Proteins

• CHARMM36m + TIP3P*: Nat Methods 2017;14:71

General Organic Ligands

• CGenFF: J. Comput. Chem. 2010, 31, 671. Automatic forcefield generator.

D.E.Shaw

Proteins

• a99SBdisp from D.E.Shaw viparr, modified amber99SB-ILDN + TIP4P-D: Proc Natl Acad Sci 2018;115: E4758
• J Chem Theory Comput 2020;16:2494
• OPLS3e: Desmond from D.E.Shaw

OPLS

General Organic Ligands

• LigParGen: Automatic forcefield generator.