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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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TLDR
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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Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field
TL;DR: In this paper, the generalized Born (GB) model is used to estimate free energies of A and B form structures of DNA obtained from molecular dynamics simulations, and the results provide an account of the conformational preferences of right-handed DNA in solution.
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Experimental and Computational Studies of Choline Chloride-Based Deep Eutectic Solvents
TL;DR: In this article, three choline chloride-based DESs are simulated using molecular dynamics to study the hydrogen bonding interactions of the system, and three hydrogen bond donors (HBDs) are studied in order to determine the changes in the hydrogen bond interactions when the HBD is different in the DES.
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Locked Nucleic Acid (LNA) Recognition of RNA: NMR Solution Structures of LNA:RNA Hybrids
TL;DR: It is suggested that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.
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Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
Jay L. Banks,George A. Kaminski,Ruhong Zhou,Daniel T. Mainz,Bruce J. Berne,Richard A. Friesner +5 more
TL;DR: In this paper, a polarizable force field for peptides was developed using all-atom OPLS (OPLS-AA) nonelectrostatic terms and electrostatics based on a fluctuating charge model and fit to ab initio calculations of polarization responses.
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Molecular Dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-Related Inhibitors: Mechanism for Binding and Drug Resistance
Tingjun Hou and,Ron X. Yu +1 more
TL;DR: In this article, the binding of amprenavir to both of the wild-type and the drug-resistant V82F/I84V mutant of the HIV-1 protease was investigated by molecular dynamics simulations and was compared to those of two inhibitors in development.
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.