Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

ABSTRACT: A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition

SUBMITTER: Li X 

PROVIDER: S-EPMC3633718 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature