Validation of an all-atom protein force field: from dipeptides to larger peptides

Article Abstract:

The study demonstrates how the applicability of a modified version of AMBER force field (A94/MOD) can extend from short to large peptides. The results of the study reveals that most aspects of protein force fields are well refined and only need minor refinements to accurately reproduce experimental observations over a range of systems.

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Characterization of hydrogen bonding in a continuum solvent model

Article Abstract:

A simple approach for calculating hydrogen bonding (H-bonding) effects in molecular mechanics simulations of peptides and proteins is presented for use in the framework of the continuum solvent model. The H-bonding description is easily implemented in standard force fields, with virtually no additional computing time requirements.

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Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides

Article Abstract:

The results of improving the OPLS-AA force field for peptides by means of refitting the key Fourier torsional coefficients are discussed. A novel approach to fitting torsional parameters for electrostatically charged molecular systems is discussed, and tested on five dipeptides with charged side chains.

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