AMBER 307123 221667985 2008-06-25T15:17:35Z 193.232.68.75 /* External links */ :''This article is about a [[molecular dynamics]] application and [[Force field (chemistry)|force field]]. For more meanings of the word '''Amber''', see [[Amber (disambiguation)]].'' [[Image:Bond stretching energy.png|thumb|right|AMBER is used to minimize the bond stretching energy of this ethane molecule.]] '''AMBER''' (an [[acronym]] for '''Assisted Model Building and Energy Refinement''') is a family of [[Force field (chemistry)|force field]]s 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 [[software package|package]] that implements these force fields. It is maintained by an active collaboration 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 [[State University of New York at Stony Brook|Stony Brook University]], Ray Luo at [[UC Irvine]], and Junmei Wang at Encysive Pharmaceuticals. ==Force Field== 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. ===Functional form=== The functional form of the AMBER force field is <br> <math> V(r^N)=\sum_\mbox{bonds} \frac{1}{2} k_b (l-l_0)^2 + \sum_\mbox{angles} \frac{1}{2} k_a (\theta - \theta_0)^2</math> <blockquote> <math>+ \sum_\mbox{torsions} \frac{1}{2} V_n [1+\cos(n \omega- \gamma)]</math> <math>+\sum_{j=1} ^{N-1} \sum_{i=j+1} ^N \left\{4\epsilon_{i,j}\left[\left(\frac{\sigma_{ij}}{r_{ij}} \right)^{12} - \left(\frac{\sigma_{ij}}{r_{ij}} \right)^6 \right]+ \frac{q_iq_j}{4\pi \epsilon_0 r_{ij}}\right\} </math> </blockquote> 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 [[term (mathematics)|term]]s are: * 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. * 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 series]]. * 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. 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 [[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. ===Programs=== * '''LEaP''' is used for preparing input files for the simulation 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 [[Visual Molecular Dynamics|VMD]]. A new visualization alternative is [[Sirius visualization software|Sirius]]. * '''MM-PBSA''' allows for implicit solvent calculations on snap shots from molecular dynamics simulations ==See also== * [[Molecular dynamics]] * [[Molecular geometry]] ==References== * Duan et al. [http://dx.doi.org/10.1002/jcc.10349 A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations] Journal of Computational Chemistry Vol. 24, Issue 16. Pages 1999-2012 (2003). ==External links== * [http://amber.scripps.edu AMBER website] * [http://amber.ch.ic.ac.uk/archive/ AMBER mailing list archive] * [http://www.agilemolecule.com/Ascalaph/index.html Ascalaph] - molecular graphics and dynamics in AMBER94 [[Category:Molecular dynamics software]] [[Category:Force fields]] [[es:AMBER]] [[zh:AMBER力场]]