ArticleData in brief2021
Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.
Article in Data in brief, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Molecular dynamics insights into the interactions of biocompatible synthetic polymer composites with carbon-based nanoparticle derivatives: a comparative study of PLGA and PCL interactions with GO/rGO.Journal of computer-aided molecular design · 2025Article
- Identification of Potential Nontoxic HumanACS omega · 2025Article
- Machine learning-based screening and molecular simulations for discovering novel PARP-1 inhibitors targeting DNA repair mechanisms for breast cancer therapy.Molecular diversity · 2025Article
- Discovery of Novel DDR1 Inhibitors through a Hybrid Virtual Screening Pipeline, Biological Evaluation and Molecular Dynamics Simulations.ACS medicinal chemistry letters · 2025Article
- A Hybrid Energy-Based and AI-Based Screening Approach for the Discovery of Novel Inhibitors of AXL.ACS medicinal chemistry letters · 2025Article
- Integrating machine learning and structure-based approaches for repurposing potent tyrosine protein kinase Src inhibitors to treat inflammatory disorders.Scientific reports · 2025Article
- Aotaphenazine, a rare hydrophenazine, targets topoisomerase II with anticancer efficacy: In silico to in vitro evidence.PloS one · 2025Article
- Jiawei Duhuo Jisheng Mixture Mitigates Osteoarthritis Progression in Rabbits by Inhibiting Inflammation: A Network Pharmacology and Experimental Approach.Combinatorial chemistry & high throughput screening · 2025Article
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- Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity.International journal of molecular sciences · 2023Article
- MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories.International journal of molecular sciences · 2023Article
- Ligand-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulations of New β-Estrogen Receptor Activators with Potential for Pharmacological Obesity Treatment.Molecules (Basel, Switzerland) · 2023Article
- Nanoscale Iron-Based Metal-Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media.International journal of molecular sciences · 2023Article
- Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor.International journal of molecular sciences · 2022Article
- Novel inhibitors of the main protease enzyme of SARS-CoV-2 identified via molecular dynamics simulation-guided in vitro assay.Bioorganic chemistry · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CL
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