Journal article
Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment (vol 11, pg 2315, 2015)
Journal of chemical theory and computation, Vol.14(12), pp.6742-6743
12/01/2018
DOI: 10.1021/acs.jctc.8b00594
PMID: 30427669
Abstract
Some time after the publication of our paper,1 we became aware of a problem with our implementation of modified dihedral parameters for nucleic acids in simulations performed with the particular version of GROMACS (4.6.5) used in our work. Specifically, for reasons described below, simulations that we thought used the ?OL3 and ?OL4 parameter sets?which were designed to improve the modeling of the glycosidic dihedral angle in RNA and DNA, respectively?did not in fact correctly use those parameters. The problem is a relatively subtle one. In GROMACS, dihedral parameters are listed, along with the other bonded parameters, in a file called ffbonded.itp. In attempting to incorporate the ?OL3 and ?OL4 dihedral parameters, we added the new entries at a line in this file af ter all preexisting dihedral parameters. The preexisting dihedral parameters include a number that contain wild cards (denoted X), such as X-CT-N-X, that can be used to assign generic parameters to dihedral angles involving a variety of atom types. At the time that we conducted our work, we were under the impression that entries containing wild cards would be overridden by more specifically defined dihedral entries that appeared later in the list of dihedral parameters. For example, we assumed that the wild-card-containing dihedral entry XCT- N-X would be overridden by ?OL3s entries for the more specifically defined dihedral entry OS-CT-N-C4. Unfortunately, however, we recently become aware that in all versions of GROMACS prior to version 5.1.3, it is the f irst set of parameters that matches to a given dihedral angle that is used, with all subsequent matches being ignored, even if those matches are more specific. This means that dihedral entries that are listed after wild-card-containing entries in the ffbonded.itp file are generally at risk of being ignored, without warning, in older versions of GROMACS. A full description of this feature of GROMACS, as discussed and resolved by its developers, can be found here: https://redmine.gromacs.org/ issues/1901; there, the developers note that in versions of GROMACS prior to version 5.1.3, the importance of dihedral parameter ordering does not seem to be documented. The relative ordering of wild-card-containing and specific dihedral entries is no longer an issue in versions 5.1.3 and later. In these newer versions, the entry with the most specific match to the atom types in question is used.
Details
- Title: Subtitle
- Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment (vol 11, pg 2315, 2015)
- Creators
- Reid F. BrownCasey T. AndrewsAdrian H. Elcock
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.14(12), pp.6742-6743
- Publisher
- Amer Chemical Soc
- DOI
- 10.1021/acs.jctc.8b00594
- PMID
- 30427669
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Number of pages
- 2
- Language
- English
- Date published
- 12/01/2018
- Academic Unit
- Molecular Physiology and Biophysics; Physics and Astronomy; Biochemistry and Molecular Biology
- Record Identifier
- 9984288718702771
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