Dear Users,
Recently, two new force field corrections for RNA chi torsion angles have
been introduced i.e. OL3(Banas et al) and YIL (yildirim et al). While there
are some papers which have tested these two parameters on individual
nucleosides and -tides as well as short RNA structural motifs like
kink-turns and tetraloops with time scale from 300-1000ns(approx), i just
want to know whether these parameters have been tested on whole and intact
structures like riboswitches or RNA aptamers. It has been proposed that
both the parameters work well in the range of ~300-400ns long simulation,
but if one tries to take a complete structure with all non-watson crick
base-pairs and other unusual geometries into account, wouldn't the
behaviour of the 2 parameters change?
Also, if one wants to test these two parameters on a structure like
riboswitch, then what should be the appropriate time scale for a simulation?
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Received on Wed Jul 18 2012 - 03:30:02 PDT
