AMBER
From wiki.gromacs.org
AMBER (Assisted Model Building and Energy Refinement) refers both to a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs.
- Using AMBER Force Field in GROMACS
- AMBER 94/99 - several AMBER protein and nucleic acid force fields are available with complete documentation. Please see the ffamber website at http://folding.stanford.edu/ffamber/ for details, as our ports and accompanying documentation will be updated there until integration into future GROMACS distributions.
- AMBER Force Fields
- AMBER Programs
- ANTECHAMBER/GAFF - Generalized Amber Force Field (GAFF) which is supposed to provide parameters suitable for small molecules that are compatible with the AMBER protein/nucleic acid force fields. It is available either together with AMBER, or through the antechamber package, which is also distributed separately. There is a script available for converting AMBER systems (set up, for example, with GAFF) to GROMACS (amb2gmx.pl), but it requires an AMBER installation to work.
