Force field parametrization is an iterative procedure that consumes time and resources particularly when the optimization targets condensed phase properties. Recently, new side chain torsion parameters were introduced into the CHARMM protein force field and conformational properties of the individual side chains were evaluated using explicit solvent protein simulations. Due to size of the system and need for extended MD simulations to attain convergence, it became evident that a smaller model system was required to allow for iterative optimization of side chain parameters prior to their validation in full protein simulations. Among possible models systems, (Ala)4-X-(Ala)4 includes  interactions of the side chain, X, with the backbone beyond the adjacent peptide bonds and its small size requires relatively short times to converge when using enhanced sampling methodologies . Presented will be systematic evaluation of (Ala)4-X-(Ala)4 as a model system of side chain conformational properties, including comparisons with results from full protein simulations. Discussion will include the role of backbone conformation on side-chain conformational sampling and use of the Hamiltonian Replica Exchange enhanced sampling approach exploiting the CMAP utility in CHARMM.

(Ala)4-X-(Ala)4 as a model system for the optimization of the [chi]1 and [chi]2 amino acid side chain dihedral empirical force field parameters

244th National Meeting (2012)

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