Gromacs

AMBER

    Table of contents
    No headers

    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.

    As of GROMACS version 4.5, the following seven AMBER force fields are natively supported:

    • AMBER94
    • AMBER96
    • AMBER99
    • AMBER99SB
    • AMBER99SB-ILDN
    • AMBER03
    • AMBERGS

    Older GROMACS versions need a separate installation of the ffamber ports:

    • Using AMBER Force Field in GROMACS - known as the "ffamber ports," a number of AMBER force fields, complete with documentation.
    • AMBER Force Fields - background about the AMBER force fields
    • AMBER Programs - information about the AMBER suite of programs for molecular simulation
    • 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.
    • ACPYPI - Tutorial on how to generate topologies for proteins and ligands to use with AMBER

    Using the ffamber ports with GROMACS requires that the input structure files adhere to the AMBER nomenclature for residues.  Problematic residues involve termini (prefixed with N and C), lysine (either LYN or LYP), histidine (HID, HIE, or HIS), and cysteine (CYN or CYX).  Please see the ffamber documentation.  The ACPYPI tutorial linked above provides several commands to make the necessary replacements, but it is also useful for those unfamiliar with sed replacements to understand a bit more thoroughly what's going on!

    Page last modified 14:21, 2 Aug 2010 by mabraham