J
James W. Caldwell
Researcher at University of California, San Francisco
Publications - 15
Citations - 34257
James W. Caldwell is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Solvation & Molecular dynamics. The author has an hindex of 13, co-authored 15 publications receiving 30518 citations. Previous affiliations of James W. Caldwell include Stanford University.
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Journal ArticleDOI
Development and testing of a general amber force field.
TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan,Chun Wu,Shibasish Chowdhury,Mathew C. Lee,Guoming Xiong,Wei Zhang,Rong Yang,Piotr Cieplak,Piotr Cieplak,Ray Luo,Tai-Sung Lee,Tai-Sung Lee,James W. Caldwell,Junmei Wang,Peter A. Kollman +14 more
TL;DR: 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.
Journal ArticleDOI
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
David A. Pearlman,David A. Case,James W. Caldwell,Wilson S. Ross,Thomas E. Cheatham,Steve DeBolt,David M. Ferguson,George Seibel,Peter A. Kollman +8 more
TL;DR: 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.
Journal ArticleDOI
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
TL;DR: In this article, a methodology to derive RESP charges for molecular mechanical models that include "lone pairs" on lone-pair donor sites and atom-centered polarizabilities was developed.