scholarly journals Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au–S Bonds

2018 ◽  
Vol 15 (1) ◽  
pp. 613-624 ◽  
Author(s):  
Zdenek Futera ◽  
Jochen Blumberger
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Charmm Force Field

Additive CHARMM36 Force Field for Nonstandard Amino Acids

2021 ◽  
Author(s):  
Anastasia Croitoru ◽  
Sang-Jun Park ◽  
Anmol Kumar ◽  
Jumin Lee ◽  
Wonpil Im ◽  
...  
Keyword(s):  
Amino Acids ◽  
Force Field

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

scholarly journals Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

2019 ◽  
Author(s):  
Siva Dasetty ◽  
John K. Barrows ◽  
Sapna Sarupria
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Force Field ◽  
Force Fields ◽  
Principal Component ◽  
Free Energies ◽  
Adsorbed State ◽  
Free Energy Of Adsorption ◽  
Density Based Clustering ◽  
Structural Preferences

<div> <div> <div> <p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </p> </div> </div> </div>

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

scholarly journals Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

2021 ◽  
Vol 23 (1) ◽  
pp. 473
Author(s):  
Olgun Guvench ◽  
Devon Martin ◽  
Megan Greene
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Dynamics ◽  
Explicit Solvent ◽  
Conformational Properties ◽  
Adaptive Biasing ◽  
Charmm Force Field ◽  
Ring Puckering ◽  
Dynamics Simulations

The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.

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