W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model
Result description
Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.
Keywords
correlated molecular calculationsgaussian-basis setsdensity-functional theorypartial atomic chargesforce-fieldab-initio
The result's identifiers
Result code in IS VaVaI
Alternative codes found
RIV/61989592:15640/21:73607214 RIV/61989592:15310/21:73607214
Result on the web
DOI - Digital Object Identifier
Alternative languages
Result language
angličtina
Original language name
W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model
Original language description
Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.
Czech name
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Czech description
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Classification
Type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
1549-9626
Volume of the periodical
17
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
15
Pages from-to
3495-3509
UT code for WoS article
000661542700023
EID of the result in the Scopus database
2-s2.0-85108021210
Basic information
Result type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
OECD FORD
Physical chemistry
Year of implementation
2021