Assisted Model Building with Energy Refinement (AMBER) | |
---|---|
Original author(s) | Peter Kollman, Version1: +Paul Weiner. Version 2: + U Chandra Singh; V3. + David Pearlman, James Caldwell, William Ross, Thomas Cheatham, Stephen Debolt, David Ferguson, George Seibel; Later versions: David Case, Tom Cheatham, Ken Merz, Adrian Roitberg, Carlos Simmerling, Ray Luo, Junmei Wang, Ross Walker |
Developer(s) | University of California, San Francisco |
Initial release | 1981 |
Stable release | Amber23, AmberTools23 [1] / April 21, 2023 |
Written in | C, C++, Fortran |
Operating system | Windows, OS X, Linux, Unix, CNK |
Platform | x86, Nvidia GPUs, Blue Gene |
Size | Varies |
Available in | English |
Type | Molecular dynamics |
License | Amber: Proprietary AmberTools: GPL, public domain, other open-source |
Website | ambermd |
Assisted Model Building with Energy Refinement (AMBER) is the name of a widely used molecular dynamics software package originally developed by Peter Kollman's group at the University of California, San Francisco. It has also, subsequently, come to designate a family of force fields for molecular dynamics of biomolecules that can be used both within the AMBER software suite and with many modern computational platforms.
The original version of the AMBER software package was written by Paul Weiner as a post-doc in Peter Kollman's laboratory, and was released in 1981. [2]
Subsequently, U Chandra Singh expanded AMBER as a post-doc in Kollman's laboratory, adding molecular dynamics and free energy capabilities.
The next iteration of AMBER was started around 1987 by a group of developers in (and associated with) the Kollman lab, including David Pearlman, David Case, James Caldwell, William Ross, Thomas Cheatham, Stephen DeBolt, David Ferguson, and George Seibel. [3] This team headed development for more than a decade and introduced a variety of improvements, including significant expansion of the free energy capabilities, accommodation for modern parallel and array processing hardware platforms (Cray, Star, etc.), restructuring of the code and revision control for greater maintainability, PME Ewald summations, tools for NMR refinement, and many others.
Currently, AMBER is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at University of Pittsburgh.
The term AMBER force field generally refers to the functional form used by the family of AMBER force fields. This form includes several parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.
The functional form of the AMBER force field is [4]
Despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential relative to position.
The meanings of right hand side terms are:
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.)
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. [5]
The recommended force fields are verified to work well with each other when mixed and matched. ff19SB works best with the OPC water model; ff14SBonlysc works well with OPC3 or implicit solvent; ff14SB is tuned for TIP3P.
AMBER has integrated modified amino acid changes into phosaa14SB/phosaa19SB and ff14SB_modAA. Parameters from ff15ipq are useful for unnatural modifications. Official guidance recommends mixing in these parameters to the main model.
The AMBER software suite provides a set of programs to apply the AMBER forcefields to simulations of biomolecules. It is written in the programming languages Fortran 90 and C, with support for most major Unix-like operating systems and compilers. Development is conducted by a loose association of mostly academic labs. New versions are released usually 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 and allows use in any number of computers under the same affiliation. AMBER 10 was priced at US$500 for non-commercial and US$20,000 for commercial organizations. AMBER 24 is priced at US$0 for academic/non-profit/government, US$500 for commercial hardware benchmarking and compiler-testing purposes, US$2000 for not-for-profit computing centers with non-profit users, and US$25000 for industrial purposes (US$20000 for recurring customers). Use by for-profit computing centers requires special licensing deals.
AmberTools is a collection of tools that work well with AMBER as well as each other. It is available free of change. Most components are available under GNU GPL, some others as GNU LGPL, public domain, or a different open-source license.
AMBER includes no visualizing abilities, which is commonly performed with Visual Molecular Dynamics (VMD). Ptraj is now unsupported as of AmberTools 13.
1. Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C.; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; et al. (2003). "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations". Journal of Computational Chemistry. 24 (16): 1999–2012. doi:10.1002/jcc.10349. PMID 14531054. S2CID 283317.