Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method

Jakalian, Araz; Bush, Bruce L.; Jack, D. B.; Bayly, Christopher I.

doi:10.1002/(sici)1096-987x(20000130)21:2<132::aid-jcc5>3.0.co;2-p

Cited by 1,438 publications

(711 citation statements)

References 43 publications

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“…135 Among the protocols they tested, RESP charges from HF/6-31G* performed the best, with a RMS error of 1.04 kcal/mol in hydration free energy of 44 compounds, closely followed (RMSE=1.10 kcal/mol) by semi-empirical charges from an AM1-BCC method tuned to reproduce HF/6-31G* charges. 136,137 Recent calculations using Amber GAFF parameters for 504 neutral molecules reported a RMSE of 1.24 kcal/mol and a correlation of 0.89 between simulation and experimental values. 138 …”

Section: Resultsmentioning

confidence: 99%

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Ren

Ponder

2011

J. Chem. Theory Comput.

437

690

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An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

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Section: Resultsmentioning

confidence: 99%

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Ren

Ponder

2011

J. Chem. Theory Comput.

437

690

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“…79,80 For the evaluation of the MM energy functional, the general Amber force field (GAFF) 81 was used where the corresponding MM parameters were generated by the A program 82 using the AM1-BCC charge scheme. 83,84 The electrostatic and van der Waals terms were not cut off, and only those bonded terms were retained which contained at least one MM or MM host atom. Residual charges which come from zeroing the charges of the QM and MM host atoms were distributed equally among all MM atoms.…”

Section: A Computational Detailsmentioning

confidence: 99%

Exact density functional and wave function embedding schemes based on orbital localization

Hégely

Nagy

Ferenczy

et al. 2016

The Journal of Chemical Physics

115

161

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Articles you may be interested in (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed. Published by AIP Publishing.[http://dx

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“…Charges for standard residues in RNAs are taken from AMBER ff14SB 80, 81 and charges for nonstandard residues, including ligand for the A-riboswitch, are calculated using the ANTECHAMBER module with the AM1-BCC charges. 82, 83 In order to test the sensitivity of the different partial charge assignment methods, we also use PDB2PQR method 84 to calculate the partial charges for the 58-nt fragment of rRNA with AMBER99, 85 CHARMM22, 86 or PARSE 87 force fields.…”

Section: The Pctbi Modelmentioning

confidence: 99%

Predicting Ion Effects in an RNA Conformational Equilibrium

et al. 2017

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We develop a partial charge-based Tightly Bound Ion (PCTBI) model for the ion effects in RNA folding. Based on the Monte Carlo Tightly Bound Ion (MCTBI) approach, the model can account for ion fluctuation and correlation effects, and can predict the ion distribution around the RNA. Furthermore, unlike the previous coarse-grained RNA charge models, where negative charges are placed on the phosphates only, the current new model considers the detailed all-atom partial charge distribution on the RNA. Thus, the model not only keeps the advantage of the MCTBI model but also has the potential to provide important detailed information unattainable by the previous MCTBI models. For example, the model predicts the reduction in ion binding upon protein binding and ion-induced conformational switches. For Hepatitis C virus (HCV) genomic RNA, the model predicts a Mg2+-induced stabilization of a kissing motif for a cis-acting regulatory element in the genomic RNA. Extensive theory-experiment comparisons support the reliability of the theoretical predictions. Therefore, the model may serve as a robust starting point for further development of an accurate method for ion effects in RNA conformational equilibrium and RNA-cofactor interactions.

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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method

Cited by 1,438 publications

References 43 publications

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Exact density functional and wave function embedding schemes based on orbital localization

Predicting Ion Effects in an RNA Conformational Equilibrium

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