Literature DB >> 24684585

Update to the general amber force field for small solutes with an emphasis on free energies of hydration.

Joakim P M Jämbeck1, Alexander P Lyubartsev.   

Abstract

An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.

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Year:  2014        PMID: 24684585     DOI: 10.1021/jp4111234

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  10 in total

Review 1.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

2.  A fast and high-quality charge model for the next generation general AMBER force field.

Authors:  Xibing He; Viet H Man; Wei Yang; Tai-Sung Lee; Junmei Wang
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

3.  Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies.

Authors:  Andreas Mecklenfeld; Gabriele Raabe
Journal:  J Comput Aided Mol Des       Date:  2019-11-28       Impact factor: 3.686

4.  Using MD Simulations To Calculate How Solvents Modulate Solubility.

Authors:  Shuai Liu; Shannon Cao; Kevin Hoang; Kayla L Young; Andrew S Paluch; David L Mobley
Journal:  J Chem Theory Comput       Date:  2016-03-02       Impact factor: 6.006

5.  Preserving the Integrity of Empirical Force Fields.

Authors:  Asuka A Orr; Suliman Sharif; Junmei Wang; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2022-08-02       Impact factor: 6.162

6.  Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

Review 7.  Markov state models of biomolecular conformational dynamics.

Authors:  John D Chodera; Frank Noé
Journal:  Curr Opin Struct Biol       Date:  2014-05-16       Impact factor: 6.809

8.  GAFF/IPolQ-Mod+LJ-Fit: Optimized force field parameters for solvation free energy predictions.

Authors:  Andreas Mecklenfeld; Gabriele Raabe
Journal:  ADMET DMPK       Date:  2020-06-28

9.  Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins.

Authors:  Artyom D Glova; Igor V Volgin; Victor M Nazarychev; Sergey V Larin; Sergey V Lyulin; Andrey A Gurtovenko
Journal:  RSC Adv       Date:  2019-11-27       Impact factor: 3.361

10.  Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.

Authors:  Noor Asidah Mohamed; Richard T Bradshaw; Jonathan W Essex
Journal:  J Comput Chem       Date:  2016-10-19       Impact factor: 3.376

  10 in total

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