scholarly journals CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

2007 ◽  
Vol 28 (2) ◽  
pp. 495-507 ◽  
Author(s):  
Evelyn Mayaan ◽  
Adam Moser ◽  
Alexander D. MacKerell ◽  
Darrin M. York
Keyword(s):  
Force Field ◽  
Reactive Intermediates ◽  
Charmm Force Field ◽  
Force Field Parameters

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

Revised CHARMM force field parameters for iron-containing cofactors of photosystem II

2017 ◽  
Vol 39 (1) ◽  
pp. 7-20 ◽  
Author(s):  
Suliman Adam ◽  
Michaela Knapp-Mohammady ◽  
Jun Yi ◽  
Ana-Nicoleta Bondar
Keyword(s):  
Photosystem Ii ◽  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters

Optimization of CHARMM force field parameters for the chalcone fragment

2012 ◽  
Vol 55 (12) ◽  
pp. 2580-2586
Author(s):  
Hui Zhang ◽  
Yuan Yao ◽  
XiaoLi Qi ◽  
ZeSheng Li
Keyword(s):  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters

Investigating the Interfacial Interactions Between Organic and Inorganic Phases and Their Influence on the Mechanics of Organic Phase in Natural Bone

2006 ◽  
Vol 975 ◽  
Author(s):  
Rahul Bhowmik ◽  
Kalpana S Katti ◽  
Dinesh R Katti
Keyword(s):  
Force Field ◽  
Deformation Behavior ◽  
Collagen Molecule ◽  
Natural Bone ◽  
Close Proximity ◽  
Nanocomposite System ◽  
Charmm Force Field ◽  
C And N ◽  
Force Field Parameters ◽  
Smd Simulations

ABSTRACTBone is a highly ordered nanocomposite system consisting primarily of organic (collagen) and inorganic (hydroxyapatite(HAP)) phases. The nanocrystals of hydroxyapatite (HAP) mineralize at specific locations in bone. The collagen molecule in bone has C and N terminals which are known as C and N telopeptides. We have performed Molecular Dynamics (MD) and Steered MD (SMD) simulations to study the interface between HAP (mineral) and collagen with N-terminal telopeptides. The force field parameters for HAP were taken from our previous study and the force field parameters for collagen with telopeptides were taken from CHARMm force field. We have investigated the detailed conformation of telopeptides interacting with specific surfaces of mineral and the interface between HAP and collagen. The load-deformation behavior of collagen is obtained with SMD simulations. It has been found that the load deformation behavior of collagen is different when in close proximity of and interacting with HAP.

scholarly journals CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs

2017 ◽  
Vol 72 ◽  
pp. 32-42 ◽  
Author(s):  
Yue Yu ◽  
Ishan A. Fursule ◽  
Landon C. Mills ◽  
Derek L. Englert ◽  
Brad J. Berron ◽  
...  
Keyword(s):  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters

The determination of CHARMM force field parameters for the Mg2+ containing HIV-1 integrase

2018 ◽  
Vol 711 ◽  
pp. 1-7 ◽  
Author(s):  
Thommas Musyoka ◽  
Özlem Tastan Bishop ◽  
Kevin Lobb ◽  
Vuyani Moses
Keyword(s):  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Hiv 1

CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes

2007 ◽  
Vol 4 (1) ◽  
pp. 107-115 ◽  
Author(s):  
Jeffery B. Klauda ◽  
Bernard R. Brooks
Keyword(s):  
Force Field ◽  
Charmm Force Field ◽  
Force Field Parameters
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