I am currently working in a project that needs MD simulation of a small RNA hairpin. I am currently trying it on GROMACS but it seems to be protein based, hence am facing several issues. Is there any software that is designed for the same?
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$\begingroup$ Welcome to the site @AKB (I hope you register here also). How long is your small RNA ? How long do you need your simulation to go on? Also if you could provide how have you searched for those programs we could help you to refine the search query too $\endgroup$– llrsJan 29, 2019 at 8:51
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2 Answers
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AMBER has force fields specifically for viewing RNA free energy and structural dynamics. Specifically, AMBERff99 is useful for RNA analysis. It is fairly easy to use and a comprehensive software for your analysis. It has plenty of tutorials from basic to advanced usage, as well as many publications. A specific publication related to your question can be found at
doi: 10.1016/j.bpj.2009.10.040
But in general, the J Phys Chem B is relevant to MD studies.
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Google found this review that might be of interest: https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427
Here is a link to a free full-text version: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/29297679/
The authors "here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field."
Hope this helps.
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1$\begingroup$ I've added a link to a free version, and provided an abstract from the abstract. $\endgroup$ Feb 1, 2019 at 10:23