W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00554903" target="_blank" >RIV/68081707:_____/21:00554903 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61989592:15640/21:73607214 RIV/61989592:15310/21:73607214

Výsledek na webu

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.0c00976" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.0c00976</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.0c00976" target="_blank" >10.1021/acs.jctc.0c00976</a>

Jazyk výsledku

angličtina

Název v původním jazyce

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

<a href="/cs/project/GA20-16554S" target="_blank" >GA20-16554S: Molekulové modelování RNA molekul a jejích komplexů: Úloha strukturní dynamiky</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2021

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

1549-9626

Svazek periodika

17

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

15

Strana od-do

3495-3509

Kód UT WoS článku

000661542700023

EID výsledku v databázi Scopus

2-s2.0-85108021210