The Amber 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,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.
Recommended Force Fields
Note: Be careful adopting a “mix and match” strategy for different components. The recommended choices are designed to work well together, and have been fairly extensively tested. Use of other combinations requires a deeper knowledge of the nature and origin of force fields. Recommended force fields are below:
| Molecule/Ion Type | Force Field |
|---|---|
| protein | ff19SB |
| DNA | OL21 |
| RNA | OL3 |
| carbohydrates | GLYCAM_06j |
| lipids | lipids21 |
| organic molecules (usually ligands) | gaff2 |
| ions | •should be matched to water model; see force fields for ions for further discussion |
| water model | •should be matched to atomic ions; common water models include tip3p, spc/e, tip4pew, and OPC |
More Force Field Information
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.
Accessing the Amber Force Fields
All Amber force field parameter files can be obtained by
downloading AmberTools24, and extracting
the .tar file. Parameter files will be in the
$AMBERHOME/dat/leap directory tree.
- list of leaprc files available -
$AMBERHOME/dat/leap/cmd - list of lib/off files available -
$AMBERHOME/dat/leap/lib - list of frcmod/dat files available -
$AMBERHOME/dat/leap/parm
In order to add a parameter set into Leap, you will need both a lib file and a frcmod file. The leaprc files are premade scripts that call up the recommended combinations.
In-Depth Description of Amber Force Field Files
For an in-depth description of different force field file components, see Chapter 14.1 of the Amber Reference Manual.
Using the Amber force fields in other software packages:
- Using the Amber force fields in Accelrys programs (via AmberFFC).
- Using the Amber force field in Gaussian QM/MM calculations.
- Using the Amber force field in NAMD (UIUC documentation).
- Using the Amber force field in NAMD (Rutgers documentation).
- Using the Amber force field in CHARMM (from Jeff Klauda).
- Using the Amber force field in GROMACS and CHARMM (via parmed).
- Using the Amber force field in GROMACS (via ffamber).
- Using the Amber force field in X-plor
- Using the Amber force field in MOLDEN; (see also this link.)
- Using the Amber force field in desmond (Preliminary version)
- Using the Amber force field in openMM
- Using the Amber force field in MOE