David A. Case

The Amber biomolecular simulation programs

Abstract We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program...

Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization

We have developed the IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water. The method involves ite...

Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high r...

Development and testing of a general amber force field

Abstract We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic a...

Automatic atom type and bond type perception in molecular mechanical calculations

Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields wit...

A new force field for molecular mechanical simulation of nucleic acids and proteins

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new force field for molecular mechanical simulation of nucleic acids and proteinsScott J. Weiner, Peter A. Kollman, David A. Case, ...

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Force Fields for Protein Simulations

Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf

Abstract Estimating protein–protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the c...