Literature DB >> 32610969

Driving torsion scans with wavefront propagation.

Yudong Qiu1, Daniel G A Smith2, Chaya D Stern3, Mudong Feng4, Hyesu Jang1, Lee-Ping Wang1.   

Abstract

The parameterization of torsional/dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms. To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values. However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses. In this paper, we propose a systematic and versatile workflow called TorsionDrive to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development. The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described. The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.

Year:  2020        PMID: 32610969      PMCID: PMC7320903          DOI: 10.1063/5.0009232

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  31 in total

1.  The case for steric repulsion causing the staggered conformation of ethane.

Authors:  F Matthias Bickelhaupt; Evert Jan Baerends
Journal:  Angew Chem Int Ed Engl       Date:  2003-09-15       Impact factor: 15.336

2.  OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

Authors:  Edward Harder; Wolfgang Damm; Jon Maple; Chuanjie Wu; Mark Reboul; Jin Yu Xiang; Lingle Wang; Dmitry Lupyan; Markus K Dahlgren; Jennifer L Knight; Joseph W Kaus; David S Cerutti; Goran Krilov; William L Jorgensen; Robert Abel; Richard A Friesner
Journal:  J Chem Theory Comput       Date:  2015-12-01       Impact factor: 6.006

3.  Generating Efficient Quantum Chemistry Codes for Novel Architectures.

Authors:  Alexey V Titov; Ivan S Ufimtsev; Nathan Luehr; Todd J Martinez
Journal:  J Chem Theory Comput       Date:  2012-11-12       Impact factor: 6.006

4.  Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Authors:  Alberto Pérez; Iván Marchán; Daniel Svozil; Jiri Sponer; Thomas E Cheatham; Charles A Laughton; Modesto Orozco
Journal:  Biophys J       Date:  2007-03-09       Impact factor: 4.033

5.  Effect of the damping function in dispersion corrected density functional theory.

Authors:  Stefan Grimme; Stephan Ehrlich; Lars Goerigk
Journal:  J Comput Chem       Date:  2011-03-01       Impact factor: 3.376

6.  ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.

Authors:  Chuan Tian; Koushik Kasavajhala; Kellon A A Belfon; Lauren Raguette; He Huang; Angela N Migues; John Bickel; Yuzhang Wang; Jorge Pincay; Qin Wu; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2019-12-03       Impact factor: 6.006

7.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

Authors:  Stefan Grimme; Jens Antony; Stephan Ehrlich; Helge Krieg
Journal:  J Chem Phys       Date:  2010-04-21       Impact factor: 3.488

8.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

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

9.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

10.  Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Phys Chem Lett       Date:  2019-12-30       Impact factor: 6.475

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  4 in total

1.  Automation of AMOEBA polarizable force field for small molecules: Poltype 2.

Authors:  Brandon Walker; Chengwen Liu; Elizabeth Wait; Pengyu Ren
Journal:  J Comput Chem       Date:  2022-07-01       Impact factor: 3.672

2.  Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

Authors:  Yudong Qiu; Daniel G A Smith; Simon Boothroyd; Hyesu Jang; David F Hahn; Jeffrey Wagner; Caitlin C Bannan; Trevor Gokey; Victoria T Lim; Chaya D Stern; Andrea Rizzi; Bryon Tjanaka; Gary Tresadern; Xavier Lucas; Michael R Shirts; Michael K Gilson; John D Chodera; Christopher I Bayly; David L Mobley; Lee-Ping Wang
Journal:  J Chem Theory Comput       Date:  2021-09-22       Impact factor: 6.578

3.  Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations.

Authors:  Mudong Feng; Michael K Gilson
Journal:  Phys Chem Chem Phys       Date:  2021-03-25       Impact factor: 3.676

4.  Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.

Authors:  Mudong Feng; Germano Heinzelmann; Michael K Gilson
Journal:  Sci Rep       Date:  2022-08-10       Impact factor: 4.996

  4 in total

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