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From: Sangeetha B <sangeetha.bicpu.edu.in>

Date: Fri, 13 Dec 2013 23:30:18 +0530

Thanks for the suggestion. I will surely try it out.

But, clustering depends on the number of clusters and the critical distance

that we set in cpptraj command?

for ex. if i give a trajectory of 100 structures and the number of clusters

as 10, it is going to give me 10 clusters.

My output will depend on the choice of the input.

Is there any way to decide the best number of clusters and the critical

distance?

Also, the clustering depends on the algorithm used and there is no least

squares fitting algorithm in AMBER as used by Daggett.

On Fri, Dec 13, 2013 at 11:12 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:

*> Hi
*

*>
*

*> I looked at Daggett's paper and I understand what they did, I think.
*

*>
*

*> There are no such tools in amber per se, but it should be rather trivial
*

*> for you use what we already have to get the needed data. Basically, they
*

*> compute average structures every 5 ps (cpptraj can do this, maybe with
*

*> an external loop driver), and then you compute the RMSD of a structure
*

*> at time t with the structure at t-DeltaT (5 ps in the example above).
*

*> Those rmsd should be 'small' while you are in one cluster, and jump up
*

*> when you change clusters. It is clear that the plot in Valerie's paper
*

*> is made up, they day as much. It is a graphical representation with no
*

*> real data.
*

*>
*

*> Associated with this, you might want to use the clustering method in
*

*> cpptraj as:
*

*>
*

*> 1. cluster form frames 1 to N
*

*> 2. cluster from frames 1 to N+1
*

*>
*

*> if the +1 frame is in a different (new) cluster, then somewhere between
*

*> N and N+1 there was a transition state. That is effectively what
*

*> Daggett is doing.
*

*>
*

*> Adrian
*

*>
*

*>
*

*> On 12/13/13 12:28 PM, Sangeetha B wrote:
*

*> > 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
*

*> >>
*

*> >
*

*> >
*

*>
*

*> --
*

*> Dr. Adrian E. Roitberg
*

*>
*

*> Colonel Allan R. and Margaret G. Crow Term Professor.
*

*> Quantum Theory Project, Department of Chemistry
*

*> University of Florida
*

*> roitberg.ufl.edu
*

*> 352-392-6972
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Fri, 13 Dec 2013 23:30:18 +0530

Thanks for the suggestion. I will surely try it out.

But, clustering depends on the number of clusters and the critical distance

that we set in cpptraj command?

for ex. if i give a trajectory of 100 structures and the number of clusters

as 10, it is going to give me 10 clusters.

My output will depend on the choice of the input.

Is there any way to decide the best number of clusters and the critical

distance?

Also, the clustering depends on the algorithm used and there is no least

squares fitting algorithm in AMBER as used by Daggett.

On Fri, Dec 13, 2013 at 11:12 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:

-- Thank you, With regards, B. Sangeetha _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Dec 13 2013 - 10:30:02 PST

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