ArticleJournal of computational chemistry2020
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 81 citations in OpenAlex.
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- Enhancing Empirical Energy Functions Using Physics- and Machine Learning-Based Extensions: Structure, Dynamics and Spectroscopy of Modified Benzenes.Journal of computational chemistry · 2025Article
- Molecular permeation through large pore channels: computational approaches and insights.The Journal of physiology · 2025Review
- Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans.Journal of computational chemistry · 2025Article
- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- The interplay of polarizable water and protein in the activation of the M2 channel.Frontiers in pharmacology · 2025Article
- Employing Metadynamics to Predict the Membrane Partitioning of Carboxy-2The journal of physical chemistry. B · 2024Article
- Distinct binding conformations of epinephrine with α- and β-adrenergic receptors.Experimental & molecular medicine · 2024Article
- Exploring the Use of a Lipopeptide in Dipalmitoylphosphatidylcholine Monolayers for Enhanced Detection of Glyphosate in Aqueous Environments.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Broadening access to small-molecule parameterization with the force field toolkit.The Journal of chemical physics · 2024Article
- CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.Nature communications · 2024Article
- FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation.The journal of physical chemistry. B · 2024Article
- Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.The journal of physical chemistry. B · 2024Article
- Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam.Journal of molecular modeling · 2024Article
- Effect of Acetylation on the Nanofibril Formation of Chitosan from All-Atom De Novo Self-Assembly Simulations.Molecules (Basel, Switzerland) · 2024Article
- In-Cell Dynamics: The Next Focus of All-Atom Simulations.The journal of physical chemistry. B · 2023Review
- Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding.Nature communications · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Accurate force-field (FF) parameters are key to reliable prediction of properties obtained from molecular modeling (MM) and molecular dynamics (MD) simulations. With ever-widening applicability of MD simulations, robust parameters need to be generated for a wider range of chemical species. The CHARMM General Force Field program (CGenFF, https://cgenff.umaryland.edu/) is a tool for obtaining initial parameters for a given small molecule based on analogy with the available CGenFF parameters. However, improvement of these parameters is often required and performing their optimization remains tedious and time consuming. In addition, tools for optimization of small molecule parameters in the context of the Drude polarizable FF are not yet available. To overcome these issues, the FFParam package has been designed to facilitate the parametrization process. The package includes a graphical user interface (GUI) created using Qt libraries. FFParam supports Gaussian and Psi4 for performing quantum mechanical calculations and CHARMM and OpenMM for MM calculations. A Monte Carlo simulated annealing (MCSA) algorithm has been implemented for automated fitting of partial atomic charge, atomic polarizabilities and Thole scale parameters. The LSFITPAR program is called for automated fitting of bonded parameters. Accordingly, FFParam provides all the features required for generation and analysis of CHARMM and Drude FF parameters for small molecules. FFParam-GUI includes a text editor, graph plotter, molecular visualization, and text to table converter to meet various requirements of the parametrization process. It is anticipated that FFParam will facilitate wider use of CGenFF as well as promote future use of the Drude polarizable FF.
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