Insights into the phosphatase and the synthase activities of human bisphosphoglycerate mutase: a quantum mechanics/molecular mechanics simulation

2014 ◽  
Vol 16 (9) ◽  
pp. 3946 ◽  
Author(s):  
Wen-Ting Chu ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Bisphosphoglycerate Mutase

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching

scholarly journals Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase

Biochemistry ◽  
2017 ◽  
Vol 56 (48) ◽  
pp. 6377-6388 ◽  
Author(s):  
Jitrayut Jitonnom ◽  
Jon I. Mujika ◽  
Marc W. van der Kamp ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Ring Opening

scholarly journals Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute–solvent interactions

2014 ◽  
Vol 16 (38) ◽  
pp. 20639-20649 ◽  
Author(s):  
Petr Štěpánek ◽  
Petr Bouř
Keyword(s):  
Amino Acids ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Electronic Spectra ◽  
Aromatic Amino Acids ◽  
Molecular Structures ◽  
Solvent Interactions ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Electronic spectra provide a wealth of information on molecular structures. We demonstrate a very satisfactory agreement between experimental and modeled spectra, as obtained by combined molecular mechanics/quantum mechanics computations for three aromatic amino acids.

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