AMBER
Encyclopedia
Force field (chemistry)
In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
for molecular dynamics
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
of biomolecules originally developed by the late Peter Kollman
Peter Kollman
Peter Andrew Kollman was a professor of chemistry and pharmaceutical chemistry at the University of California, San Francisco....
's group at the University of California, San Francisco
University of California, San Francisco
The University of California, San Francisco is one of the world's leading centers of health sciences research, patient care, and education. UCSF's medical, pharmacy, dentistry, nursing, and graduate schools are among the top health science professional schools in the world...
. AMBER is also the name for the molecular dynamics software package
Software package (installation)
In package management systems, which are commonly used with Linux-based operating systems, a package is a specific piece of software which the system can install and uninstall....
that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University
Rutgers University
Rutgers, The State University of New Jersey , is the largest institution for higher education in New Jersey, United States. It was originally chartered as Queen's College in 1766. It is the eighth-oldest college in the United States and one of the nine Colonial colleges founded before the American...
, Tom Cheatham at the University of Utah
University of Utah
The University of Utah, also known as the U or the U of U, is a public, coeducational research university in Salt Lake City, Utah, United States. The university was established in 1850 as the University of Deseret by the General Assembly of the provisional State of Deseret, making it Utah's oldest...
, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling
Carlos Simmerling
Carlos Simmerling is a full Professor of Chemistry at the State University of New York at Stony Brook. Simmerling received his Bachelor of Arts in 1991 from the University of Illinois at Chicago and then his Doctorate in 1994 from the same institution...
at Stony Brook University
State University of New York at Stony Brook
The State University of New York at Stony Brook, also known as Stony Brook University, is a public research university located in Stony Brook, New York, on the North Shore of Long Island, about east of Manhattan....
, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.
Force field
The term "AMBER force fieldForce field (chemistry)
In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
" 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.
Functional form
The functional form of the AMBER force field is
Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect to position.
The meanings of right hand side terms
Term (mathematics)
A term is a mathematical expression which may form a separable part of an equation, a series, or another expression.-Definition:In elementary mathematics, a term is either a single number or variable, or the product of several numbers or variables separated from another term by a + or - sign in an...
are:
- First term (sumSUMSUM can refer to:* The State University of Management* Soccer United Marketing* Society for the Establishment of Useful Manufactures* StartUp-Manager* Software User’s Manual,as from DOD-STD-2 167A, and MIL-STD-498...
ming over bonds): represents the energy between covalently bonded atoms. This harmonic (ideal spring) force is a good approximation near the equilibrium bond length, but becomes increasingly poor as atoms separate. - Second term (summing over angles): represents the energy due to the geometry of electron orbitals involved in covalent bonding.
- Third term (summing over torsions): represents the energy for twisting a bond due to bond order (e.g. double bonds) and neighboring bonds or lone pairs of electrons. Note that a single bond may have more than one of these terms, such that the total torsional energy is expressed as a Fourier seriesFourier seriesIn mathematics, a Fourier series decomposes periodic functions or periodic signals into the sum of a set of simple oscillating functions, namely sines and cosines...
. - Fourth term (double summation over
and 
): represents the non-bonded energy between all atom pairs, which can be decomposed into van der WaalsVan der Waals forceIn physical chemistry, the van der Waals force , named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral...
(first term of summation) and electrostaticElectrostaticsElectrostatics is the branch of physics that deals with the phenomena and properties of stationary or slow-moving electric charges....
(second term of summation) energies.
The form of the van der Waals energy is calculated using the equilibrium distance (
) and well depth (
). The factor of 
ensures that the equilibrium distance is 
. The energy is sometimes reformulated in terms of 
, where 
, as used e.g. in the implementation of the softcore potentials.The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge (or in the case of parameter sets that employ lone pairs, a small number of point charges.)
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 by Rob Woods for simulating carbohydrates.
Software
The AMBER software suite provides a set of programs for applying the AMBER forcefields to simulations of biomolecules. It is written in Fortran 90 and CC (programming language)
C is a general-purpose computer programming language developed between 1969 and 1973 by Dennis Ritchie at the Bell Telephone Laboratories for use with the Unix operating system....
with support for most major Unix-like
Unix-like
A Unix-like operating system is one that behaves in a manner similar to a Unix system, while not necessarily conforming to or being certified to any version of the Single UNIX Specification....
systems and compilers. Development is conducted by a loose association of mostly academic labs. New versions are generally released in the spring of even numbered years; AMBER 10 was released in April 2008. 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 simulation programs
- Antechamber automates the process of parameterizing small organic molecules using GAFF
- SANDER (Simulated Annealing with NMR-Derived Energy Restraints) 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 VMDVisual Molecular Dynamics- External links :* * *...
. A new visualization alternative is SiriusSirius visualization softwareSirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins...
. - MM-PBSA allows for implicit solvent calculations on snap shots from molecular dynamics simulations