Assisted Model Building with Energy Refinement (AMBER) is a set of molecular force fields for biomolecular molecular dynamics, which has a wide range of applications in the field of biomacromolecular simulation computing. The AMBER force field was initially created specifically to calculate protein and nucleic acid systems, and the information used to determine its force field parameters came from experimental values. The AMBER force field's content was afterward continuously improved and gradually developed as a result of its widespread use. A force field system is created that may be applied to simulation computations of organic small molecules, biological macromolecules, and biological macromolecules.
In general, the advantage of the AMBER force field lies in the calculation of biological macromolecules. The AMBER force field has been implemented in numerous common computing software programs at this time. Alfa Chemistry is able to offer its clients MD simulation services using the AMBER force field.
Fig 1. The physical models for the AMBER molecular mechanics force field. Atoms and bonds are shown. (A) The physical model for bond stretching, (B) the model for angle bending, (C) the model for angle torsional energy, and (D) the model for electrostatics and Van der Waals forces. (Ngan S-C, et al. 2008)
AMBER force field usually refers to the functional form used by the AMBER force field family. This force field's potential energy function condition is less complicated, calls for fewer parameters, and requires less computation.
The AMBER force field calculates the bond length stretching and bending energies using the resonant oscillator model, the dihedral angle torsion energies using the Fourier series form, the van der Waals force using the Lennard-Jones potential, and the electrostatic interactions using the Coulomb formula. The expression for potential energy is provided by.
Fig 2. The functional form of the AMBER force field. (Boyd N.J, et al. 2015)
In addition to AMBER software, Alfa Chemistry uses a variety of well-known computing software programs that apply the AMBER force field for analysis and simulation, including Sybyl, Cerius2, Insight II, MOE, and HyperChem.
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AMBER is suitable for cohesive phase simulation of proteins and nucleic acids, with little support for organic small molecules. The following versions are included:
- ff12: The difference from ff10 is that the parameters of the backbone and side chain twist terms of proteins have been further corrected to better fit the experiments. The parameters for nucleic acids are unchanged. This is the best amber force field available.
- ff10: A collection of various parameter patches to ff99. The parameters for proteins are the same as ff99SB.
- ff99SBildn: Patch with improved side chain parameters for isoleucine, leucine, aspartate, asparagine of ff99SB.
- ff99SBnmr: Patch with modified backbone parameters of ff99SB based on NMR data.
- ff03.r1: A modified version of ff99 force field. Obtained charge by continuous dielectric model to show solvent polarizable effect, modified protein phi, psi backbone parameters, reduced preference for helical conformation. Nucleic acid parameters are unchanged with respect to ff99.
- ff02: Polarizable version of ff99 force field, adding polarizable dipoles to the atoms.
- ff02EP: The ff02 force field is based on the ff02 force field and adds point charges off-center to atoms such as oxygen, nitrogen, and sulfur to show the lone pair electron effect.
- ff99SB: The protein dihedral angle parameter of ff99 was modified and the ratio of the distribution between secondary structures was improved, also solving the problem of the glycine backbone parameter.
- ff99SBildn: Patch to modify the amino acid side chain parameters based on ff99SB.
- ff99SBnmr: Patch to modify the backbone torsion term parameters on the basis of ff99SB to better match the NMR data.
- ff94: Suitable for solvent environment. Charge is obtained from RESP HF/6-31G*.
- ff84: The earliest AMBER force field for simulating the combined atomic force field of nucleic acids and proteins. Not recommended, but still useful for simulations in vacuum or with distance-dependent dielectric constants.
Alfa Chemistry provides global customers with fast, professional, high-quality MD simulation services at competitive prices, which can reduce the cost of late-stage experiments. We need to evaluate each project before we can determine the corresponding analysis plan and price. If you are interested in our services, please contact us for more details.
- Boyd N.J, et al. (2015). "Optimization of the GAFF Force Field to Describe Liquid Crystal Molecules: the Path to A Dramatic Improvement in Transition Temperature Predictions." Phys. Chem. Chem. Phys. 17: 24851-24865.
- Ngan S-C, et al. (2008). "Scoring Functions for De Novo Protein Structure Prediction Revisited." Methods in Molecular Biology. 413: 243-281.