Reconciling MA′AT and molecular dynamics models of linkage conformation in oligosaccharides

MA′AT conformational models of the phi torsion angles of O -glycosidic linkages differ from those obtained from MD simulation. To determine the source of the discrepancy, MA′AT analyses were performed using DFT-derived equations obtained with and without psi constraints. The resulting phi models wer...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2020-07, Vol.22 (26), p.14454-14457
Main Authors: Meredith, Reagan J, Woods, Robert J, Carmichael, Ian, Serianni, Anthony S
Format: Article
Language:English
Subjects:
Computer simulation
Constraint modelling
Coupling (molecular)
Couplings
Molecular dynamics
Oligosaccharides
Parameterization
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Summary:MA′AT conformational models of the phi torsion angles of O -glycosidic linkages differ from those obtained from MD simulation. To determine the source of the discrepancy, MA′AT analyses were performed using DFT-derived equations obtained with and without psi constraints. The resulting phi models were essentially the same, indicating a force-field problem. Circular standard deviations (CSDs) were found to provide reliable estimates of torsional averaging. MA′AT conformational models of the phi torsion angles of O -glycosidic linkages differ from those obtained from MD simulation.
ISSN:1463-9076
1463-9084
DOI:10.1039/d0cp01389g