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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>
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--
--------------------------------------------------------------
Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
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Received on Thu Sep 20 2018 - 09:00:05 PDT
