Additive CHARMM force field for naturally occurring modified ribonucleotides
Open Access
- 3 February 2016
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 37 (10) , 896-912
Abstract
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 data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.Keywords
Funding Information
- NIH (GM070855, and GM051501)
- Swedish Research Council
- China Scholarship Council
- Karolinska Institutet Board of Doctoral Education
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