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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related… Expand
Development and testing of a general amber force field
- Junmei Wang, R. Wolf, J. Caldwell, P. Kollman, D. Case
- Chemistry, Computer Science
- J. Comput. Chem.
- 15 July 2004
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 acids, and has parameters for… Expand
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides. Expand
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
- P. Kollman, I. Massova, +12 authors T. Cheatham
- Chemistry, Medicine
- Accounts of chemical research
- 4 October 2000
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation… Expand
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…
The development, current features, and some directions for future development of the AMBER package of computer programs are described, embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations. Expand
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The… Expand
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the… Expand
A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char
We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the… Expand
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 potential (RESP) approach… Expand