scholarly journals Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations

2018 ◽  
Vol 14 (2) ◽  
pp. 784-798 ◽  
Author(s):  
Anna Pavlova ◽  
Jerry M. Parks ◽  
James C. Gumbart
Keyword(s):  
Force Field ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Force Field Parameters

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Thomas Hamelryck ◽  
Jan H Jensen
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Jan H Jensen ◽  
Thomas Hamelryck
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

Derivation of Force Field Parameters, and Force Field and Quantum Mechanical Studies of Layered α- and γ-Zirconium Phosphates

1999 ◽  
Vol 38 (19) ◽  
pp. 4249-4255 ◽  
Author(s):  
Giulio Alberti ◽  
Antonio Grassi ◽  
Giuseppe M. Lombardo ◽  
Giuseppe C. Pappalardo ◽  
Riccardo Vivani
Keyword(s):  
Force Field ◽  
Quantum Mechanical ◽  
Zirconium Phosphates ◽  
Force Field Parameters ◽  
Mechanical Studies

scholarly journals Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

Introducing QUBE: Quantum Mechanical Bespoke Force Fields for Protein Simulations

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
Conformational Preferences ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete QUantum mechanical BEspoke (QUBE) protein force field, which derives non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. Overall, with several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

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