Peter A. Kollman

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucle...

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelChristopher I....

A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

Abstract Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third‐generation point...

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic pot...

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

AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed‐memory hypercube computers

Abstract A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long‐r...

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

<scp>AMBER</scp>: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

Abstract We describe a computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is s...