Development and testing of a general amber force field
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Summary
A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
- Type
- article
- Published
- 2004-07-15
- Cited by
- 17,833
- References
- 32
- Access
- Open access
- OpenAlex
- https://openalex.org/W2147993766
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18734898
Keywords
Force field (fiction), Chemistry, Computational chemistry, Molecule, Intermolecular force
References
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- Encyclopedia of computational chemistry
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- Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
- Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
- Molecular structures of gas‐phase polyatomic molecules determined by spectroscopic methods
- An improved force field (MM4) for saturated hydrocarbons
- AMBER torsional parameters for the peptide backbone
- Automatic parameterization of force field by systematic search and genetic algorithms
- Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method
- Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree–Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree–Fock results
- The MM3 force field for amides, polypeptides and proteins
- A comparison of conformational energies calculated by several molecular mechanics methods
- A second generation force field for the simulation of proteins
- Molecular Modelling: Principles and Applications
- Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics
- How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
- Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
- Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
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- Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations.
- Solid-state NMR and MD simulations of the antiviral drug amantadine solubilized in DMPC bilayers.
- Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.
- The implementation of a fast and accurate QM/MM potential method in Amber
- Linear absorbance of the pheophorbide-a butanediamine dendrimer P(4) in solution: computational studies using a mixed quantum classical methodology.
- Insights into docking and scoring neuronal α4β2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations
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- Small-molecule ligands of GD2 ganglioside, designed from NMR studies, exhibit induced-fit binding and bioactivity.
- Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design
- New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights
- On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study.
- NMR and molecular modeling reveal key structural features of synthetic nodulation factors.
- Adsorption behavior of 17α-ethynylestradiol onto soils followed by fluorescence spectral deconvolution.
- Is N-acetyl-d-glucosamine a rigid 4C1 chair?
- AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
- Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link.
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