scholarly journals Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4in ZIF-8

2016 ◽  
Vol 2016 ◽  
pp. 1-6
Author(s):  
Phannika Kanthima ◽  
Pikul Puphasuk ◽  
Tawun Remsungnen
Keyword(s):  
Force Field ◽  
Md Simulations ◽  
Binding Energies ◽  
Parameters Optimization ◽  
Interaction Energies ◽  
Intermolecular Force ◽  
Amber Force Field ◽  
De Algorithm ◽  
Force Field Parameters ◽  
Structural Behaviors

The differential evolution (DE) algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4and 2-methylimidazolate ([C4N2H5]−) using quantum binding energies of CH4-[C4N2H5]−complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD) simulations of CH4molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.

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

scholarly journals Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

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

Uncertainty Quantification in MD Simulations. Part II: Bayesian Inference of Force-Field Parameters

2012 ◽  
Vol 10 (4) ◽  
pp. 1460-1492 ◽  
Author(s):  
F. Rizzi ◽  
H. N. Najm ◽  
B. J. Debusschere ◽  
K. Sargsyan ◽  
M. Salloum ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Force Field ◽  
Uncertainty Quantification ◽  
Md Simulations ◽  
Force Field Parameters

scholarly journals Data for Molecular Dynamics Simulations of Escherichia Coli Cytochrome Bd Oxidase with the Amber Force Field

2021 ◽  
Author(s):  
Surl-Hee Ahn ◽  
Christian Seitz ◽  
Vinicius Cruzeiro ◽  
James McCammon ◽  
Andreas Goetz
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Force Field ◽  
Drug Targets ◽  
Food Poisoning ◽  
Md Simulations ◽  
Data Bank ◽  
Low Oxygen ◽  
Amber Force Field ◽  
E Coli

<div> <div> <div> <div> <p>Cytochrome <i>bd</i>-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the <i>Mycobacterium tuberculosis (Mtb)</i> bacterium that causes tuberculosis (TB) in humans, the <i>Vibrio cholerae</i> bacterium that causes cholera, the <i>Pseudomonas aeruginosa</i> bacterium that contributes to antibiotic resistance and sepsis, and the <i>Campylobacter jejuni</i> bacterium that causes food poisoning. <i>Escherichia coli (E. coli)</i> is another organism exhibiting the cytochrome <i>bd</i> oxidase. Since it has the highest sequence identity to <i>Mtb</i> (36 %) and we are ultimately interested in finding drug targets for TB, we have built parameters for the <i>E. coli bd </i>oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome <i>bd</i>-type oxidases (heme b<sub>558</sub>, heme b<sub>595</sub>, and heme d) along with their axial ligands. This data report includes the parameter files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions. </p> </div> </div> </div> </div>

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.

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

2007 ◽  
Vol 3 (4) ◽  
pp. 1464-1475 ◽  
Author(s):  
Raviprasad Aduri ◽  
Brian T. Psciuk ◽  
Pirro Saro ◽  
Hariprakash Taniga ◽  
H. Bernhard Schlegel ◽  
...  
Keyword(s):  
Force Field ◽  
Modified Nucleosides ◽  
Amber Force Field ◽  
Naturally Occurring ◽  
Force Field Parameters
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