Ligand Force Fields

Amber is designed to work with several simple types of force fields, although it is most commonly used with parametrizations developed by Peter Kollman and his co-workers and “descendents”. The traditional parametrization uses fixed partial charges, centered on atoms. For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.

GAFF2 Force Fields (recommended)

For a general force field, for organic molecules like ligands, the recommended force field is gaff2. Since 2015, the second generation of GAFF (GAFF2) has been released to the public via the AMBER program and AmberTools. A description can be found in the footer of the released gaff2.dat file and with the completion of the remaining work on representative chemical space expansion and some parameter improvement, the development detail is soon to be submitted for publication. In a very brief summary, compared to GAFF, GAFF2 has updated the bonded parameters to reproduce molecular geometries, vibrational spectra, and potential energy surfaces from higher level quantum mechanics (QM) calculations on more model compounds, and updated the non-bonded parameters to better reproduce ab initio interaction energies and experimental neat liquid properties.

In AmberTools24, there is a new charge model (ABCG2) for GAFF2:
Ref: He, X., Man, V.H., Yang, W., Lee,T-S. and J. Wang J. Chem. Phys., 2020, 153, 114502.

See Chapter 15 in the Amber 2024 Reference Manual for more information about this.

Pre-built small molecule force fields using GAFF2

Many small molecules are present in the PDB, and we have built Amber files for about 29,000 of these, which can be downloaded at https://ambermd.org/downloads/amber_geostd.tar.bz2. These files may be useful if you know the PDB residue code for your ligand or other small molecule. See the README file in the tarfile for more information.

RED Database

This is a database of RESP charges and force field libraries for small molecules and biological molecular fragments.

REDDB (Resp \ Esp charge Data Base) is maintained by P. Cieplak, F. Dupradeau and co-workers. (Hint: click on "List Projects"; "co-factor_biochemistry" has entries that are commonly requested by users.)