ArticleThe Journal of chemical physics2020
A fast and high-quality charge model for the next generation general AMBER force field.
Article in The Journal of chemical physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 367 papers.
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Who cites it
367 citing papers in PubMed.
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- 2-Oxoindoline-based hydroxamic acids: novel HDAC inhibitors with promising anticancer activity.RSC advances · 2026Article
- In Silico Isomerization Produces Apt Negative Data for VHTS Validation.Journal of chemical information and modeling · 2026Article
- ARG128-associated recognition of nobiletin by BACE1 revealed by triplicate molecular dynamics, MM-GBSA, and residue-level decomposition.Molecular diversity · 2026Article
- Oxygen-Dependent Light-Induced Lipid Membrane Perturbation by TLD1433 as a Potential Contributor to Phototoxicity.Inorganic chemistry · 2026Article
- Synthesis of Some Oxime Derivatives as Novel Elastase Inhibitors: Molecular Dynamics Studies and Computational Insight.Chemistry & biodiversity · 2026Article
- Decoding the allosteric grammar of protein kinases: A dual-stream framework integrating protein language models and energy landscape frustration analysis.Protein science : a publication of the Protein Society · 2026Article
- Novel Benzofuranyl Chalcones With Antileishmanial Activity: Synthesis, Structure-Activity Relationships, and Computational Target Hypothesis Studies.ChemMedChem · 2026Article
- A biocatalytic platform for the stereoselective synthesis of diverse atropisomeric compounds using engineered metalloenzymes.Science advances · 2026Article
- DFT design of PORSC advances · 2026Article
- Toward Predicting Solubility of Arbitrary Solutes in Arbitrary Solvents: Prediction of Density and Refractive Index Using Machine Learning Algorithms with Global Sensitivity Analysis.Organic process research & development · 2026Article
307 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary task is to accurately predict the affinity and selectivity of receptor-ligand binding. The atomic partial charges in GAFF and the second generation of GAFF (GAFF2) were originally developed with the quantum mechanics derived restrained electrostatic potential charge, but in practice, users usually adopt an efficient charge method, Austin Model 1-bond charge corrections (AM1-BCC), based on which, without expensive ab initio calculations, the atomic charges could be efficiently and conveniently obtained with the ANTECHAMBER module implemented in the AMBER software package. In this work, we developed a new set of BCC parameters specifically for GAFF2 using 442 neutral organic solutes covering diverse functional groups in aqueous solution. Compared to the original BCC parameter set, the new parameter set significantly reduced the mean unsigned error (MUE) of hydration free energies from 1.03 kcal/mol to 0.37 kcal/mol. More excitingly, this new AM1-BCC model also showed excellent performance in the solvation free energy (SFE) calculation on diverse solutes in various organic solvents across a range of different dielectric constants. In this large-scale test with totally 895 neutral organic solvent-solute systems, the new parameter set led to accurate SFE predictions with the MUE and the root-mean-square-error of 0.51 kcal/mol and 0.65 kcal/mol, respectively. This newly developed charge model, ABCG2, paved a promising path for the next generation GAFF development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.