Additive CHARMM force field for naturally occurring modified ribonucleotides.
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ABSTRACT:
SUBMITTER: Xu Y
PROVIDER: S-EPMC4801715 | biostudies-literature | 2016 Apr
REPOSITORIES: biostudies-literature
Publications
Additive CHARMM force field for naturally occurring modified ribonucleotides.
Xu You Y Vanommeslaeghe Kenno K Aleksandrov Alexey A MacKerell Alexander D AD Nilsson Lennart L
Journal of computational chemistry 20160203 10
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target dat ...[more]
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