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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Received on Thu Sep 20 2018 - 08:30:04 PDT
