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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.Abstract:
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 intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactionsread more
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CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations
Thomas D. Kühne,Marcella Iannuzzi,Mauro Del Ben,Vladimir V. Rybkin,Patrick Seewald,Frederick Stein,Teodoro Laino,Rustam Z. Khaliullin,Ole Schütt,Florian Schiffmann,Dorothea Golze,Jan Wilhelm,Sergey Chulkov,Mohammad Hossein Bani-Hashemian,Valéry Weber,Urban Borštnik,Mathieu Taillefumier,Alice Shoshana Jakobovits,A. Lazzaro,Hans Pabst,Tiziano Müller,Robert Schade,Manuel Guidon,Samuel Andermatt,Nico Holmberg,Gregory K. Schenter,Anna Hehn,Augustin Bussy,Fabian Belleflamme,Gloria Tabacchi,Andreas Glöß,Michael Lass,Iain Bethune,Christopher J. Mundy,Christian Plessl,Matthew Watkins,Joost VandeVondele,Matthias Krack,Jürg Hutter +38 more
TL;DR: CP2K as discussed by the authors is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems, especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations.
Journal ArticleDOI
New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects
Bryan Marten,Kyungsun Kim,Christian Cortis,‖,⊥ and,Richard A. Friesner,Robert B. Murphy# and,Murco N. Ringnalda,Barry Honig +6 more
TL;DR: In this article, the authors present self-consistent reaction field (SCRF) calculations, utilizing correlated ab initio quantum mechanics, of aqueous solvation free energies for a large data base of molecular solutes.
Journal ArticleDOI
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.
TL;DR: Modifications to the Cornell et al. force field are tested in molecular dynamics simulations of mononucleosides and double helices of DNA and RNA (to assess helical and sequence specific structural properties) and lead to improved agreement with experimental data.
Journal ArticleDOI
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
Irina Massova,Peter A. Kollman +1 more
TL;DR: In this paper, a computational scanning mutagenesis method was proposed to identify the 'hotspots' in binding interfaces from a single trajectory of a wild type complex, which can be also used as a tool to optimize the interacting species for the binding, or as a ranking procedure in high throughput screening.
Journal ArticleDOI
The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building
François-Yves Dupradeau,Adrien Pigache,Thomas Zaffran,Corentin Savineau,Rodolphe Lelong,Nicolas Grivel,Dimitri Lelong,Wilfried Rosanski,Piotr Cieplak +8 more
TL;DR: These tools perform charge derivation in an automatic and straightforward way for non-polarizable charge models and incorporates charges into a force field library, readily usable in molecular dynamics computer packages.
References
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The MIDAS display system
TL;DR: At the core of MIDAS is a hierarchical database system, designed specifically for macromolecules, that is both compact in its storage requirements and fast in its data access.