Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

2004 ◽  
Vol 55 (3) ◽  
pp. 620-634 ◽  
Author(s):  
Mathew C. Lee ◽  
Yong Duan
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Scoring Function ◽  
Generalized Born ◽  
Amber Force Field ◽  
Solvent Model ◽  
Dynamics Simulations

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.

scholarly journals Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

Data in Brief ◽  
2016 ◽  
Vol 8 ◽  
pp. 1209-1214 ◽  
Author(s):  
Longhua Yang ◽  
Åge A. Skjevik ◽  
Wen-Ge Han Du ◽  
Louis Noodleman ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Cytochrome C Oxidase ◽  
Amber Force Field ◽  
Dynamics Simulations

scholarly journals Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field

Data in Brief ◽  
2021 ◽  
Vol 38 ◽  
pp. 107401
Author(s):  
Surl-Hee Ahn ◽  
Christian Seitz ◽  
Vinícius Wilian D. Cruzeiro ◽  
J. Andrew McCammon ◽  
Andreas W. Götz
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amber Force Field ◽  
Cytochrome Bd ◽  
Dynamics Simulations ◽  
Cytochrome Bd Oxidase

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

Ab initio based force field and molecular dynamics simulations of crystalline TATB

2004 ◽  
Vol 120 (15) ◽  
pp. 7059-7066 ◽  
Author(s):  
Richard H. Gee ◽  
Szczepan Roszak ◽  
Krishnan Balasubramanian ◽  
Laurence E. Fried
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations
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