New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

2005 ◽  
Vol 26 (8) ◽  
pp. 818-826 ◽  
Author(s):  
Akifumi Oda ◽  
Noriyuki Yamaotsu ◽  
Shuichi Hirono
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Heme Iron ◽  
Cytochrome P450s ◽  
Simplified Models ◽  
Amber Force Field ◽  
Force Field Parameters

Determination of AMBER Force Field Parameters for Thioester by Quantum Chemical Calculations

2013 ◽  
Vol 42 (10) ◽  
pp. 1206-1208 ◽  
Author(s):  
Akifumi Oda ◽  
Shuichi Fukuyoshi ◽  
Ryoichi Nakagaki ◽  
Ohgi Takahashi
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Amber Force Field ◽  
Force Field Parameters

scholarly journals Comparison of different approaches to derive classical bonded force-field parameters for a transition metal cofactor: a case study for non-heme iron site of ectoine synthase

2021 ◽  
Vol 140 (8) ◽  
Author(s):  
Justyna Andrys ◽  
Johann Heider ◽  
Tomasz Borowski
Keyword(s):  
Transition Metal ◽  
Force Field ◽  
Metal Ion ◽  
Geometry Optimization ◽  
Heme Iron ◽  
Energy Structure ◽  
Test Case ◽  
Amber Force Field ◽  
Force Field Parameters ◽  
And Function

AbstractComputational investigations into the structure and function of metalloenzymes with transition metal cofactors require proper preparation of the model, which requires obtaining reliable force field parameters for the cofactor. Here, we present a test case where several methods were used to derive amber force field parameters for a bonded model of the Fe(II) cofactor of ectoine synthase. Moreover, the spin of the ground state of the cofactor was probed by DFT and post-HF methods, which consistently indicated the quintet state is lowest in energy and well separated from triplet and singlet. The performance of the obtained force field parameter sets, derived for the quintet spin state, was scrutinized and compared taking into account metrics focused on geometric features of the models as well as their energetics. The main conclusion of this study is that Hessian-based methods yield parameters which represent the geometry around the metal ion, but poorly reproduce energy variance with geometrical changes. On the other hand, the energy-based method yields parameters accurately reproducing energy-structure relationships, but with bad performance in geometry optimization. Preliminary tests show that admixing geometrical criteria to energy-based methods may allow to derive parameters with acceptable performance for both energy and geometry.

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

2016 ◽  
Vol 56 (4) ◽  
pp. 811-818 ◽  
Author(s):  
Suqing Zheng ◽  
Qing Tang ◽  
Jian He ◽  
Shiyu Du ◽  
Shaofang Xu ◽  
...  
Keyword(s):  
Force Field ◽  
Amber Force Field ◽  
Molecular Systems ◽  
Force Field Parameters

AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study

2020 ◽  
Vol 124 (5) ◽  
pp. 777-787
Author(s):  
Hamed Haghshenas ◽  
Hossein Tavakol ◽  
Bita Kaviani ◽  
Gholamhossein Mohammadnezhad
Keyword(s):  
Force Field ◽  
Biological Systems ◽  
Amber Force Field ◽  
Force Field Parameters ◽  
Systematic Derivation

A general intermolecular force field based on tight-binding quantum chemical calculations

2017 ◽  
Vol 147 (16) ◽  
pp. 161708 ◽  
Author(s):  
Stefan Grimme ◽  
Christoph Bannwarth ◽  
Eike Caldeweyher ◽  
Jana Pisarek ◽  
Andreas Hansen
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Tight Binding ◽  
Intermolecular Force

scholarly journals Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

2011 ◽  
Vol 7 (9) ◽  
pp. 2886-2902 ◽  
Author(s):  
Marie Zgarbová ◽  
Michal Otyepka ◽  
Jiří Šponer ◽  
Arnošt Mládek ◽  
Pavel Banáš ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical
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