Towards improved force fields: III. Polarization through modified atomic charges This article includes Supplementary Material available from the authors upon request or via the Internet at ftp.wiley.com/public/journals/jcc/suppmat/20/704 or http://journals.wiley.com/jcc/

Winn, Peter J.; Ferenczy, György G.; Reynolds, C. A.

doi:10.1002/(sici)1096-987x(199905)20:7<704::aid-jcc5>3.3.co;2-k

Cited by 11 publications

(15 citation statements)

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“…Although the importance of the introducing terms into MM force-field to account for electronic changes (like polarization) is now well recognized, − the study of such effects has typically been limited to the conformation energies of small molecular systems. , In contrast, this work has quantitatively compared the results of QM and MM calculations on a large and complex biomolecular system, namely, the potassium ion channel. We have found that large changes in the electronic distributions of individual amino acids in this system are induced by interactions with other nearby amino acids, particularly in the region of the selectivity filter.…”

Section: Discussionmentioning

confidence: 99%

The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

et al. 2001

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The molecular electrostatic potential inside the potassium channel protein from Streptomyces liVidans has been investigated using linear scaling semiempirical quantum chemical method, for a variety of geometries, with and without solvating water molecules. The results are compared with those given by a number of popular molecular mechanics force-fields. The difference between the quantum and molecular mechanics electrostatic potentials due to the protein exceeds 30 kcal/mol within the narrow selectivity filter of the channel and is attributed to the neglect of electronic effects, e.g., polarization, in the molecular mechanics forcefields. In particular, mutual electronic interactions between four threonine residues in the selectivity filter are found to have a large effect on the electrostatic potential. Calculations in the presence of water molecules suggest that molecular mechanics methods also overestimate the stabilization of the cation inside the ion channel. The molecular electrostatic potentials computed by molecular mechanics force-fields expressed relative to bulk water, however, reveal a much smaller error.

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Section: Discussionmentioning

confidence: 99%

The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

et al. 2001

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“…To avoid the “polarization catastrophe”, we followed the procedure of not allowing atoms separated by 3 bonds or less to polarize each other. A less obvious problem, which can be corrected for, is the corruption of the monomer charges by the polarizing effect of atoms in the same monomer unit . Here this was not a major problem and was ignored.…”

Section: Methodsmentioning

confidence: 99%

“…Stone has presented a rigorous theory for describing polarization that gives excellent results on small molecules , but, the method is not readily applicable to large biomolecular systems. For such systems, the usual simplification is to assign point charges, q , and isotropic scalar polarizabilities, α, to the atoms; here, as elsewhere, , we used the isotropic atomic polarizabilities of Miller and Savchik . The field, E , due to the point charges, q (and the induced dipoles, μ), then gives rise to induced dipoles, μ, via The induced dipoles, μ, modify the field, E , and so eq 1 is usually solved by iteration, but considerable improvement in accuracy can still be obtained without iteration − and hence with consequent savings in CPU time.…”

Section: Introductionmentioning

confidence: 99%

Classical Polarization in Hybrid QM/MM Methods

et al. 2006

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We have presented a method for modeling polarization in hybrid QM/MM calculations. The method, which expresses the induced dipoles as a set of "induced" charges, is based on the induced dipole approach and methodology for calculating potential-derived point charges from distributed multipole series. The method has the advantage that the same methodology can be used to determine the induced charges and the potential derived charges and so both sets of charges are rigorously defined within the same framework. This underlying link with the wave function makes the method particularly suitable for use in hybrid QM/MM calculations. Here we assess the importance of explicit polarization in the classical part of a QM/MM system with regard to improving the classical description and the consequent effects on the quantum description. The main advantages of the induced charge approach are that the method is readily interfaced with quantum mechanical methods and that induced charges are more readily interpreted than induced dipoles. The ease of interpretation is illustrated by analysis of the charges involved in dimeric and trimeric hydrogen bonded systems. The method for treating the MM polarization has been validated by a regression analysis of the charges induced in both the QM and MM systems against those derived from full quantum mechanical calculations. The method has also been validated using two energy decomposition approaches, which show that MM polarization makes a significant and reliable contribution to the QM - MM interaction energy in a hybrid system. The distance dependency of the induced charges is investigated in calculations on methylsuccinyl-Ala-Ala-Pro-Ala chlormethyl ketone interacting with human neutrophil elastase and propranolol interacting with asparagine residues in a model of the beta(2)-adrenergic receptor.

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“…A third type of method is built around the idea of the Drude oscillator, which introduces a mobile particle, harmonically bound to the atomic particle with an artificial force constant, and carrying a fictitious charge q D that causes the atomic charge q to be replaced by q − q D in order to preserve neutrality. A fourth type of method applies linear algebra to fit effective charges to induced dipoles. The precise classification of the aforementioned methods is actually not that important because computational schemes exist that combine features of these methods.…”

Section: Introductionmentioning

confidence: 99%

Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine

et al. 2013

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We propose a generic method to model polarization in the context of high-rank multipolar electrostatics. This method involves the machine learning technique kriging, here used to capture the response of an atomic multipole moment of a given atom to a change in the positions of the atoms surrounding this atom. The atoms are malleable boxes with sharp boundaries, they do not overlap and exhaust space. The method is applied to histidine where it is able to predict atomic multipole moments (up to hexadecapole) for unseen configurations, after training on 600 geometries distorted using normal modes of each of its 24 local energy minima at B3LYP/apc-1 level. The quality of the predictions is assessed by calculating the Coulomb energy between an atom for which the moments have been predicted and the surrounding atoms (having exact moments). Only interactions between atoms separated by three or more bonds ("1, 4 and higher" interactions) are included in this energy error. This energy is compared with that of a central atom with exact multipole moments interacting with the same environment. The resulting energy discrepancies are summed for 328 atom-atom interactions, for each of the 29 atoms of histidine being a central atom in turn. For 80% of the 539 test configurations (outside the training set), this summed energy deviates by less than 1 kcal mol(-1).

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Towards improved force fields: III. Polarization through modified atomic charges This article includes Supplementary Material available from the authors upon request or via the Internet at ftp.wiley.com/public/journals/jcc/suppmat/20/704 or http://journals.wiley.com/jcc/

Cited by 11 publications

References 0 publications

The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

Classical Polarization in Hybrid QM/MM Methods

Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine

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