Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry

2004 ◽  
Vol 108 (4) ◽  
pp. 621-627 ◽  
Author(s):  
George A. Kaminski ◽  
Harry A. Stern ◽  
B. J. Berne ◽  
Richard A. Friesner
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics

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 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.

scholarly journals Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field

2019 ◽  
Vol 123 (13) ◽  
pp. 2991-2999 ◽  
Author(s):  
R. J. Shannon ◽  
B. Hornung ◽  
D. P. Tew ◽  
D. R. Glowacki
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Mm3 Force Field

A molecular mechanics valence force field for sulfonamides derived by ab initio methods

1991 ◽  
Vol 95 (24) ◽  
pp. 9803-9811 ◽  
Author(s):  
John B. Nicholas ◽  
Robert Vance ◽  
Eric Martin ◽  
Benjamin J. Burke ◽  
A. J. Hopfinger
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Ab Initio Methods ◽  
Valence Force ◽  
Valence Force Field

An ab initio study of the electrostatics of protonated amines: application to the molecular mechanics (MM3) force field

2003 ◽  
Vol 623 (1-3) ◽  
pp. 145-158 ◽  
Author(s):  
Jennifer B Sorensen ◽  
Anita H Lewin ◽  
J Phillip Bowen
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Ab Initio Study ◽  
Protonated Amines ◽  
Mm3 Force Field

Application of a Classical Force Field for Polyvinylchloride Derived from Ab initio Calculations.

1990 ◽  
Vol 215 ◽  
Author(s):  
Peter J. Ludovice ◽  
Richard L. Jaffe ◽  
Do Y. Yoon
Keyword(s):  
Force Field ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Stochastic Dynamics ◽  
Atomic Level ◽  
Model Compounds ◽  
Dynamics Simulations ◽  
Energy Surfaces

AbstractAb initio calculations were used to characterize the inter- and intramolecular energy surfaces for polyvinylchloride (PVC) model compounds and a classical force field was fit to these energy surfaces. This new force field will be used in molecular mechanics and stochastic dynamics simulations to analyze the atomic level morphology of PVC.

Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines

1997 ◽  
Vol 18 (11) ◽  
pp. 1371-1391 ◽  
Author(s):  
Guyan Liang ◽  
Xiannong Chen ◽  
J. A. Dustman ◽  
Anita H. Lewin ◽  
J. Phillip Bowen
Keyword(s):  
Force Field ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Aliphatic Amines ◽  
Field Development ◽  
Force Field Development ◽  
Mm3 Force Field

On the use of conformationally dependent geometry trends from ab initio studies to determine empirical parameters for the CHARMm molecular mechanics force field

Proteins ◽  
1991 ◽  
pp. 379-383 ◽  
Author(s):  
Frank A. Momany ◽  
V. Joseph Klimkowski ◽  
Lothar Schäfer
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics
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