Without chi correction, any RNA will ultimately "high-anti ladder"
degrade. It is only question of time and differs from system to system.
Published papers on tetraloops were affected by that, for example
(while not reporting it....).
It does not tell that all parm99 or bsc0 RNA sims are corrupted,
in the past we have published set of papers on different RNA
motifs (Kink-turns etc) and they did not degrade on short time
scales. Most of the published papers are OK due to timescale
affordable.
We have noticed the ladders as major problem for the first time around
2009 while wokring on Hairpin ribozyme, the problem has then
been reported in 2010 Mlynsky et al JPC B.
There are some additional large-scale studies comming out soon.
We have number of tests and we have not seen any massive degradation
of the ladder type yet. I cannot tell what would happen
on milisecond time scale.
It does not tell the force field is perfect now and there
are remaining smaller problems, with impact differing
from system to system, some of them not curable with
the physical form of the force field currently used.
It is not possible to get perfect force field
by tuning just dihedrals.
One of the problems we feel is overstabilization of
stacking, discussed in Banas et al JCTC paper in the latest
JCTC issue.
It also does not invalidate parm99 or bsc0 simulations,
unless there is switch to high-anti (which can be easily
recognized by monitoring chi) they are acceptable.
If high-anti occurrs then the structure is corrupted.
Shortly, the force field is useful for many applications
but remains to have limitations which need to be further
scrutinized, reported and respected.
Best wishes, Jiri
On Wed, 18 Jul 2012, Asmita Gupta wrote:
> Date: Wed, 18 Jul 2012 15:36:21 +0530
> From: Asmita Gupta <asmita4des.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] RNA chi torsion corrections
>
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 18 2012 - 04:00:02 PDT
