Hi Arvind,
It looks to me that this approach probably may not work. When snapshot A and
B both have same rmsd values to the reference structure, it does not mean A
and B are similar, especially if the rmsd value is large. You would want to
compare snapshot A and B to see if they should be in same cluster.
We are working on ptraj clustering so that other distance metrics may be
used. Dihedral angles will be one of the possibilities. However, due to the
circularity, the sum and average of dihedral angles could be tricky. I would
suggest you still use the rmsd as the distance metric. If you have suspect
some specific angles or dihedrals, focus on those specific residues.
Hope it helps.
Jianyin Shao
On Thu, Sep 2, 2010 at 8:52 AM, Arvind <bahuroopi.gmail.com> wrote:
> Hello,
>
> I am calculating rmsd values of my snapshots with respect to a
> reference structure, in terms of several structural parameters such as
> angles/torsion angles etc. I want to cluster these rmsd values using
> different clustering algorithms. I was hoping to use the cluster
> option of ptraj module, which is part of the ambertools 1.4 package.
> However, ptraj seems to accept only the trajectory as input, and then
> produce rms | dme values, and process them further for clustering. Is
> it possible to 'tell' ptraj to directly accept an input file with time
> versus rmsd values?
>
> thanks,
> arvind
>
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Received on Fri Sep 03 2010 - 11:00:04 PDT
