Bioinformatics Molecular Dynamics

AMBER

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Molecular dynamics simulations of proteins, which began about 25 years ago, are by now widely used as tools to investigate structure and dynamics under a variety of conditions; these range from studies of ligand binding and enzyme reaction mechanisms to problems of denaturation and protein refolding to analysis of experimental data and refinement of structures.

Amber is a suite of biomolecular simulation programs used in Bioinformatics for the analysis of 3D simulations by using a set of molecular mechanical force fields for the simulation of biomolecules and are used in a variety of simulation programs. It began in the late 1970’s, and is maintained by an active development community.

The term “Amber” refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.

Amber is distributed in two parts: 

  • AmberTools20 
  • Amber20

We can use AmberTools20 without Amber20, but not vice versa. 

Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Ken Merz at Michigan State University, Adrian Roitberg at the University of Florida, Carlos Simmerling at SUNY-Stony Brook, Ray Luo at UC Irvine, Junmei Wang at the University of Pittsburgh, Ross Walker at GSK, and many others. Amber was originally developed under the leadership of Peter Kollman.

The term AMBER force field generally refers to the functional form used by the family of AMBER force fields. This form includes many parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.

To use the AMBER force field, it is necessary to have values for the parameters of the force field. A fairly large number of these parameter sets exist, and are described in detail in the AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules.

  • Peptide, protein, and nucleic acid parameters are provided by parameter sets with names starting with “ff” and containing a two digit year number, for instance “ff99”. 
  • General AMBER force field (GAFF) provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules.
  • The GLYCAM force fields have been developed by Rob Woods for simulating carbohydrates.
  • The primary force field used in the AMBER suit for lipids is lipid14. 

Over the years, Amber has discarded a number of features that were once viewed as important parts of its feature set. Some comments about what we no longer support (or support well) may help users better know what to expect from Amber. Some of the features that are now missing are these:

Preparatory programs in AMBER

  • LEaP
  • Antechamber
  • MCPB
  • Paramfit

Simulation programs in AMBER

  • NAB (Nucleic Acid Builder)
  • sander (part of Amber)
  • pmemd (part of Amber)
  • mdgx

Analysis programs in AMBER

  • Ptraj
  • Cpptraj
  • Pbsa
  • MMPBSA
  • amberlite

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