Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields

For over 20 years, the OPLS-AII Atom (OPLS-AA) force field has been efficiently used in molecular modelling studies of proteins, carbohydrates and nucleic acids. OPLS-AA is successfully applied in computer modelling of many organic compounds, including decane and shorter alkanes, but it fails when e...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Acta biochimica polonica 2020-09, Vol.67 (3), p.309-318
Hauptverfasser: Bratek, Maciej, Wojcik-Augustyn, Anna, Kania, Adrian, Majta, Jan, Murzyn, Krzysztof
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:For over 20 years, the OPLS-AII Atom (OPLS-AA) force field has been efficiently used in molecular modelling studies of proteins, carbohydrates and nucleic acids. OPLS-AA is successfully applied in computer modelling of many organic compounds, including decane and shorter alkanes, but it fails when employed for longer linear alkanes, whose chemical structure corresponds to hydrocarbon tails in phospholipids constituting cellular membranes. There have been several attempts to address this problem. In this work, we compare the ability to reproduce various condensed phase properties by six distinct sets of force field parameters which can be assigned to phospholipid hydrocarbon chains. In this comparison, we include three alternative sets of the OPLS-AA force field, as well as the commonly used CHARMM C36, Slipids, and Berger lipids' parameters.
ISSN:0001-527X
1734-154X
DOI:10.18388/abp.2020_5414