A comparison of empirical force field parameters for molecular mechanics calculations on saturated hydrocarbons

1985 ◽  
Vol 26 (44) ◽  
pp. 5355-5358 ◽  
Author(s):  
Frank A.L. Anet ◽  
Ragini Anet
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Saturated Hydrocarbons ◽  
Molecular Mechanics Calculations ◽  
Empirical Force Field ◽  
Force Field Parameters

Hydration of platinum(II) complexes: a molecular mechanics study using atom-based force-field parameters

2000 ◽  
Vol 104 (3-4) ◽  
pp. 247-251 ◽  
Author(s):  
Jacqueline Langlet ◽  
Jacqueline Berg�s ◽  
Jacqueline Caillet ◽  
Jiri Kozelka
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Force Field Parameters

Molecular Mechanics (MM3*) Force Field Parameters for Calculations on Palladium Olefin Complexes with Phosphorus Ligands

1999 ◽  
Vol 18 (22) ◽  
pp. 4574-4583 ◽  
Author(s):  
Helena Hagelin ◽  
Mats Svensson ◽  
Björn Åkermark ◽  
Per-Ola Norrby
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Phosphorus Ligands ◽  
Mm3 Force Field ◽  
Force Field Parameters

scholarly journals A force field for virtual atom molecular mechanics of proteins

2009 ◽  
Vol 106 (37) ◽  
pp. 15667-15672 ◽  
Author(s):  
Anil Korkut ◽  
Wayne A. Hendrickson
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
Molecular Mechanics Calculations ◽  
Low Degrees

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

A new spectroscopic molecular mechanics force field. Parameters for proteins

1995 ◽  
Vol 102 (21) ◽  
pp. 8586-8605 ◽  
Author(s):  
Philippe Derreumaux ◽  
Gérard Vergoten
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Force Field Parameters
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