Dear Dan,
Thanks for your reply.
I have extracted a 2D RMSD matrix but it is not helpful to understand the
conformational clustering.
The method described by Levitt, M in 1983 (J. Mol. Biol. 168, 621-657)
explains a method of RMSD analysis where after projection into 2D space,
the distances between a set of points in two-dimensional plane explains the
RMS deviations between a set of protein structures. This method can easily
identify a transition state which is generally the first structure exiting
the first cluster.
I would like to generate a plot of this nature so that a transition state
can be easily identified.
Thanks in advance.
On Fri, Dec 13, 2013 at 10:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I believe the analysis you are referring to is the construction of a graph
> where the vertices represent structures and the edges represent the RMSD
> between the structures. To my knowledge there you can't do this exactly in
> Amber, but you can calculate a 2D RMSD matrix with cpptraj or ptraj. For
> example, to look at the 2D RMSD between C-alpha atoms (cpptraj):
>
> 2drms .CA out ca2drms.gnu
>
> The ".gnu" extension tells cpptraj to write the file in gnuplot-readable
> format.
>
> Hope this helps,
>
> -Dan
>
>
>
> On Fri, Dec 13, 2013 at 7:11 AM, Sangeetha B <sangeetha.bicpu.edu.in>
> wrote:
>
> > Dear Amber users,
> >
> > I am working on protein folding/unfolding problem and I came across an
> > article
> http://www.sciencedirect.com/science/article/pii/S0022283696901722
> > .
> >
> > I am aware of the problem in identifying a transition state in protein
> > unfolding trajectory and this article (and few other related publications
> > by Valerie Daggett) identify the transition state by *Ca RMSD based
> > conformational clustering and its projection onto 3D space. *
> >
> > An analysis tool to obtain such a projection is available in CHARMM
> > (RMSDyn).
> >
> > Is it possible to perform a similar analysis using AMBER.
> >
> > Any help in this regard would be grateful.
> >
> >
> >
> > --
> > Thank you,
> >
> > With regards,
> > B. Sangeetha
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thank you,
With regards,
B. Sangeetha
Ph.D Scholar,
Centre for Bioinformatics,
Pondicherry University,
Pondicherry,
India
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Received on Fri Dec 13 2013 - 09:30:03 PST
