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AMBER (an acronym for Assisted Model Building and Energy Refinement) is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics simulation package that implements these force fields. It is maintained by an active collboration between David Case at The Scripps Research Institute, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.
Force Field
The term "AMBER force field" generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.
Parameter Sets
To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). 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 beginning with "ff" and containing a two digit year number, for instance "ff99".
GAFF (Generalized AMBER force field) 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 for simulating carbohydrates.
Software
The AMBER software suite provides a set of programs for applying the AMBER forcefields to simluations of biomolecules. It is written in Fortran 90 and C with support for most major Unix-like systems and compilers. Development is conducted by a loose association of mostly academic labs. New versions are generally released in March of even numbered years; AMBER 8 was released in March 2004. The software is available under a site-license agreement, which includes full source, currently priced at US$400 for non-commercial and US$20,000 for commercial organizations.
Programs
- LEaP is used for preparing input files for the simluation programs
- Antechamber automates the process of parameterizing small organic molecules using GAFF
- sander is the central simulation program and provides facilities for energy minimization and molecular dynamics with a wide variety of options
- pmemd is a somewhat more feature-limited reimplementation of sander by Bob Duke. It was designed with parallel processing in mind and has significantly better performance than sander when running on more than 8-16 processors
- nmode calculates normal modes
- ptraj provides facilities for numerical analysis of simulation results. AMBER does not include visualization capabilities; visualization is commonly performed with VMD
- MM-PBSA allows for implicit solvent calculations on snap shots from molecular dynamics simulation
All text used in this article is available under the GNU Free Documentation License. It uses material from the Wikipedia article "Amber".