| BEŠŠEOVÁ, Ivana, Michal OTYEPKA, Kamila RÉBLOVÁ a Jiří ŠPONER. Dependence of A-RNA simulations on the choice of the force field and salt strength. Physical Chemistry Chemical Physics. 2009, roč. 11, -, s. 10701-10711. ISSN 1463-9076. |
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@article{858800,
author = {Beššeová, Ivana and Otyepka, Michal and Réblová, Kamila and Šponer, Jiří},
article_number = {-},
keywords = {molecular dynamics methods; RNA; force field; A-form},
language = {eng},
issn = {1463-9076},
journal = {Physical Chemistry Chemical Physics},
title = {Dependence of A-RNA simulations on the choice of the force field and salt strength},
volume = {11},
year = {2009}
}
TY - JOUR
ID - 858800
AU - Beššeová, Ivana - Otyepka, Michal - Réblová, Kamila - Šponer, Jiří
PY - 2009
TI - Dependence of A-RNA simulations on the choice of the force field and salt strength
JF - Physical Chemistry Chemical Physics
VL - 11
IS - -
SP - 10701-10711
EP - 10701-10711
SN - 14639076
KW - molecular dynamics methods
KW - RNA
KW - force field
KW - A-form
N2 - We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alfa/gama t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form.
ER -
BEŠŠEOVÁ, Ivana, Michal OTYEPKA, Kamila RÉBLOVÁ a Jiří ŠPONER. Dependence of A-RNA simulations on the choice of the force field and salt strength. \textit{Physical Chemistry Chemical Physics}. 2009, roč.~11, -, s.~10701-10711. ISSN~1463-9076.
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