thank you very much Christina and Daniel!
very useful information!
On Thu, Sep 20, 2018 at 5:48 PM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hi,
>
> Each individual RNA system is fairly unique, and analysis will depend on
> what you are trying to learn from your simulations.
> To start:
> I usually do an RMSD on individual secondary structures (stem region?
> hairpin? bulge?).
> I usually look at any non-native base pairing and calculate distances for
> those.
> I usually run nastruct to see how well-behaved stem regions are.
> I evaluate the structure against any experimental data I have.
>
> For clustering, take a look at the following paper and see if it helps:
> Mg2+ binding promotes SLV as a scaffold in Varkud satellite ribozyme
> SLI-SLV kissing loop junction
> <
> https://scholar.google.com/scholar?oi=bibs&cluster=4453630380232919124&btnI=1&hl=en
> >
> C Bergonzo, TE Cheatham III - Biophysical journal, 2017
>
> I had a kissing loop junction where two RNA hairpins form Watson-Crick base
> pairs.
> The clustering commands I used in CPPTRAJ are included in the Supplementary
> Info as Script 1.
>
> Essentially, I read in my trajectory, fit on the stems, and then clustered
> using dbscan on the individual loops.
>
> Hope this helps,
> Christina
>
> On Thu, Sep 20, 2018 at 11:21 AM Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > RMSD is probably ok. You may need to be careful what residues you
> > select (e.g. you may want a few stem residues selected as well as the
> > loop, may want to exlude hydrogen atoms, etc). Another possibility
> > that comes to mind are the sugar-phosphate backbone torsions.
> >
> > Others on the list with more extensive NA clustering experience may
> > have better suggestions.
> >
> > -Dan
> >
> > PS - You may want to make use of the openmp version of cpptraj
> > (cpptraj.OMP) for clustering as it can be significantly faster on a
> > multi-core machine. Just make sure you don't use more threads than you
> > have physical cores - cpptraj does not benefit from hyperthreading.
> >
> > On Sun, Sep 16, 2018 at 4:26 AM Antonio Amber Carlesso
> > <antonio.amber.carlesso.gmail.com> wrote:
> > >
> > > Hi all,
> > > We would like to use CPPTRAJ to determine structure populations from MD
> > > simulations.
> > >
> > >
> > >
> > > Do you have any suggestion for distance metric option to be used to
> > analyze
> > > RNA stem loop and RNA dual stem loop?
> > >
> > >
> > >
> > > This tutorial (
> > http://www.amber.utah.edu/AMBER-workshop/London-2015/Cluster/
> > > ) suggests RMSD of atoms in as distance metric. Any other suggestion?
> > >
> > >
> > >
> > >
> > >
> > > Thank you!
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>
>
> --
> --------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> NIST/IBBR NRC Postdoctoral Researcher
> --------------------------------------------------------------
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Received on Thu Sep 27 2018 - 14:30:03 PDT
