Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

ABSTRACT: Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)₅. Additional optimization of the backbon

SUBMITTER: Lopes PE 

PROVIDER: S-EPMC3896220 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature