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| {{other uses|Amber (disambiguation)}}
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| [[File:Bond stretching energy.png|thumb|right|AMBER is used to minimize the bond stretching energy of this [[ethane]] molecule.]]
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| '''AMBER''' (an [[acronym]] for '''Assisted Model Building with Energy Refinement''') is a family of [[Force field (chemistry)|force fields]] for [[molecular dynamics]] of [[biomolecules]] originally developed by [[Peter Kollman]]'s group at the [[University of California, San Francisco]]. '''AMBER''' is also the name for the molecular dynamics software [[Software package (installation)|package]] that simulates these force fields. It is maintained by an active collaboration between David Case at [[Rutgers University]], Tom Cheatham at the [[University of Utah]], Tom Darden at NIEHS, Ken Merz at Florida, [[Carlos Simmerling]] at [[State University of New York at Stony Brook|Stony Brook University]], Ray Luo at [[UC Irvine]], and Junmei Wang at Encysive Pharmaceuticals.
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| == Force field ==
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| The term "AMBER [[Force field (chemistry)|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.
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| === Functional form ===
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| The functional form of the AMBER force field is<ref name="Cornell1995">{{cite journal |author=Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA |title=A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules |journal=J. Am. Chem. Soc. |volume=117 |pages=5179–5197 |year=1995 |doi=10.1021/ja00124a002}}</ref>
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| :<math>
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| V(r^N)=\sum_\text{bonds} k_b (l-l_0)^2 + \sum_\text{angles} k_a (\theta - \theta_0)^2</math>
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| <blockquote>
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| <math>+ \sum_\text{torsions} \sum_n \frac{1}{2} V_n [1+\cos(n \omega- \gamma)]</math>
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| <math>+\sum_{j=1} ^{N-1} \sum_{i=j+1} ^N f_{ij}\biggl\{\epsilon_{ij}\biggl[\left(\frac{r_{0ij}}{r_{ij}} \right)^{12} - 2\left(\frac{r_{0ij}}{r_{ij}} \right)^{6} \biggr]+ \frac{q_iq_j}{4\pi \epsilon_0 r_{ij}}\biggr\}
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| </math>
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| </blockquote>
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| 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.
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| The meanings of right hand side [[term (mathematics)|terms]] are:
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| * First term ([[sum]]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.
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| * Second term (summing over angles): represents the energy due to the geometry of electron orbitals involved in covalent bonding.
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| * 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 series]].
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| * Fourth term (double summation over <math>i</math> and <math>j</math>): represents the non-bonded energy between all atom pairs, which can be decomposed into [[van der Waals force|van der Waals]] (first term of summation) and [[electrostatics|electrostatic]] (second term of summation) energies.
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| The form of the van der Waals energy is calculated using the equilibrium distance (<math> r_{0ij} </math>) and well depth (<math> \epsilon </math>). The factor of <math>2</math> ensures that the equilibrium distance is <math> r_{0ij} </math>. The energy is sometimes reformulated in terms of <math>\sigma</math>, where <math> r_{0ij} = 2^{1/6}(\sigma)</math>, as used e.g. in the implementation of the softcore potentials.
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| 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.)
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| === Parameter sets ===
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| 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.
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| *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".
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| *GAFF (General AMBER force field) provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules.
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| *The GLYCAM force fields have been developed by Rob Woods for simulating carbohydrates.
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| == Software ==
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| 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 [[C (programming language)|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 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.
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| === Programs ===
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| * '''LEaP''' is used for preparing input files for the simulation programs
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| * '''Antechamber''' automates the process of parameterizing small organic molecules using GAFF
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| * '''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
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| * '''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
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| * '''nmode''' calculates normal modes
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| * '''ptraj''' provides facilities for numerical analysis of simulation results. AMBER does not include visualization capabilities; visualization is commonly performed with [[Visual Molecular Dynamics|VMD]].
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| * '''MM-PBSA''' allows for implicit solvent calculations on snap shots from molecular dynamics simulations
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| == See also ==
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| {{columns-list|2|
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| * [[List of software for molecular mechanics modeling]]
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| * [[Force field implementation]]
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| * [[Molecular dynamics]]
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| * [[Molecular geometry]]
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| * [[Molecular design software]]
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| * [[Molecular mechanics]]
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| * [[MDynaMix]]
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| * [[Ascalaph Designer]]
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| * [[BOSS (molecular mechanics)|BOSS]]
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| * [[CHARMM]]
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| * [[GROMACS]]
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| * [[OPLS]]
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| * [[Yasara]]
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| * [[Folding@home]]
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| }}
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| == References ==
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| {{reflist}}
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| ===Further reading===<!-- These should be moved inline. -->
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| * {{cite journal |author=Duan, ''et al.'' |last2=Wu |first2=Chun |last3=Chowdhury |first3=Shibasish |last4=Lee |first4=Mathew C. |last5=Xiong |first5=Guoming |last6=Zhang |first6=Wei |last7=Yang |first7=Rong |last8=Cieplak |first8=Piotr |last9=Luo |first9=Ray |displayauthors=8|title=A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations |journal=J Computational Chemistry |volume=24 |issue=16 |pages=1999–2012 |year=2003 |doi=10.1002/jcc.10349}}
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| == External links ==
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| * [http://ambermd.org/ AMBER website]
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| * [http://amber.ch.ic.ac.uk/archive/ AMBER mailing list archive]
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| [[Category:Fortran software]]
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| [[Category:Molecular dynamics software]]
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| [[Category:Force fields]]
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Jerrie Swoboda is what you can call me and I totally dig whom name. Managing people is my time job now. As a girl what I do like is to have croquet but I can not make it my field really. My wife and I chose to live a life in Massachusetts. Go to my web to find out more: http://circuspartypanama.com
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