Literature DB >> 31886576

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.

Anmol Kumar1, Ozge Yoluk1, Alexander D MacKerell1.   

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.
© 2019 Wiley Periodicals, Inc.

Entities:  

Keywords:  molecular dynamics; polarizable force field; quantum mechanics

Year:  2019        PMID: 31886576      PMCID: PMC7323454          DOI: 10.1002/jcc.26138

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  34 in total

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Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

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4.  GROMACS: fast, flexible, and free.

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Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

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6.  Robustness in the fitting of molecular mechanics parameters.

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7.  Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

Authors:  Christopher M Baker; Pedro E M Lopes; Xiao Zhu; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2010-03-01       Impact factor: 6.006

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Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

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10.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

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2.  Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.

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3.  Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.

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5.  Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.

Authors:  Payal Chatterjee; Mert Y Sengul; Anmol Kumar; Alexander D MacKerell
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Review 6.  Recent progress in general force fields of small molecules.

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Journal:  Curr Opin Struct Biol       Date:  2021-12-20       Impact factor: 6.809

7.  How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers.

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Review 10.  "Dividing and Conquering" and "Caching" in Molecular Modeling.

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