Molecular Modeling of Proteins pp 47-71

Part of the Methods in Molecular Biology book series (MIMB, volume 1215)

| Cite as

Current Status of Protein Force Fields for Molecular Dynamics Simulations

  • Pedro E. M. Lopes
  • Olgun Guvench
  • Alexander D. MacKerellJr.
Protocol

Abstract

The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

Key words

Force field Molecular dynamics Drude polarizable force field CHARMM AMOEBA AMBER GROMOS OPLS NAMD Electronic polarization 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Pedro E. M. Lopes
    • 1
  • Olgun Guvench
    • 2
  • Alexander D. MacKerellJr.
    • 1
  1. 1.Department of Pharmaceutical Sciences, School of PharmacyUniversity of MarylandBaltimoreUSA
  2. 2.Department of Pharmaceutical Sciences, College of PharmacyUniversity of New EnglandPortlandUSA

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