i wish to try CG simulation of siRNA, which is short duplex RNA using MARTINI force field. is there any place to find parameter files for the simulation?
Exactly why you want to study it with MARTINI? MARTINI restrain secondary structure dynamics to that of the original template. For siRNA where conformational dynamics is essential it is a serious burden. Other than that, there is no RNA parameters developed yet. DNA parameters were released by S. Marrink group recently
DOI: 10.1021/acs.jctc.5b00286
also targeting large duplexes, not small oligonucleotides. These you can do far better with all-atom MD. If you positively need it then, there was recent extension for si-RNA which you would have to build by hands:
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
http://dx.doi.org/10.1063/1.4937384
thank you very much for your thoughts Dr. Sergei. i'm in need of simulation of siRNA-Protein complex and have to choose CG due to computational cost (on a single computer). anyway, im going to try all-atom MD first.
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