Dear Dr. Daniel,
So the representative structure is, in other words, closest (to
avg.) meaningful structure. Thus, as I understand using representative
structures for RMSD analysis among the real available states, is the best
available choice.
I will try converting the PDB into Amber restart file.
Thank you very much for these suggestions and comments.
On Mon, Oct 8, 2012 at 8:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, Oct 7, 2012 at 3:24 AM, vaibhav dixit <vaibhavadixit.gmail.com>
> wrote:
> > If I guessed correctly, average structure means "average of all the
> > coordinates" in a given cluster. So the avg. structure *might not be
> > chemically meaningful* structure
>
> Yes, the average structure is made up of the coordinate positions
> averaged over all frames of the cluster, and is almost certainly not
> chemically meaningful. However, it can be useful for using as a
> reference structure for fluctuation analysis etc.
>
> > How the representative structure is chosen by the clustering algorithm?
> No
> > information is given in the manual and the original paper.
> > pubs.acs.org/doi/abs/10.1021/ct700119m
>
> >From the paper: "The representative structure is the structure which
> has the minimal sum of the squared displacements between other
> structures in the cluster and itself."
>
> > I'm having problem visualizing average PDB files generated by the
> > clustering algorithm.
> > Unusual bonds are appearing (especially in the side chains) when I load
> > these file either in pymol or vmd.
>
> Try doing output in (or alternatively converting your existing avg
> PDBs to) Amber restart format and view them that way. Since Amber
> topology contains bond info no spurious bonds will be created from
> averaged coords.
>
> Hope this is helpful.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Oct 08 2012 - 08:30:03 PDT
