this sounds good, let us know if you run into problems.
On Thu, Oct 18, 2012 at 10:37 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Amber community members,
> Please suggest on the following. Am I doing the right analysis?
> In the case that I'm applying clustering to, there is an apo-protein which
> samples 5 different dominant conformations.
> But when the ligand is bound, it appears that, out of the five only 2-3
> conformations are sampled and remain dominant. This is because of the
> stabilization of selected states by the ligand.
>
> In such a situation, earlier I tried to use average PDBs for analysis. But
> once I realized that there are usual bonds and the structure is not
> chemically meaningful, I shifted my focus towards the representative
> structures given by the clustering algorithm.
> Thus I'm now analyzing RMSD within and between the clusters of various
> complexes using the representative structures.
>
> Please suggest if this approach is good and how can I use the average PDBs
> in my analysis. I guess they are not good for RMSD analysis, are they?
>
> Thanks in advance.
>
> On Thu, Oct 18, 2012 at 7:54 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I second what Jason said about using the representative structure from
> > clustering. If the average structure is distorted, then minimizing it
> will
> > give good geometries but this can suggest that the ensemble looks like
> the
> > minimized average, which it doesn't. With distortions at least people are
> > aware that there is some diversity. Artificially getting rid of it can be
> > very misleading. For example, if you have 2 alternate conformations, and
> > the average is distorted as a result, minimizing it will make it look to
> > your audience like you only have 1 dominant conformation, and even worse,
> > it might not look like any of the actual clusters at all. I would only
> use
> > the minimized average if you have strong evidence that there is a single
> > dominant cluster with small fluctuations about the average.
> >
> >
> > On Thu, Oct 18, 2012 at 10:09 AM, <steinbrt.rci.rutgers.edu> wrote:
> >
> > > Hi Mu,
> > >
> > > Jason is absolutely correct here, but for the sake of prettier
> > > presentations, it is common to take the average structure that amber
> > gives
> > > you and conduct a short energy minimization of it. This should give
> you a
> > > chemically normal-looking structure that is at least somewhat close to
> > the
> > > average one. Alternatively, you would pick and show the snapshot from
> > your
> > > MD that has the lowest rmsd compared to the average one. I find that to
> > be
> > > a good compromise between the true average and a model that people can
> > > make sense of.
> > >
> > > Thomas
> > >
> > > On Thu, October 18, 2012 9:44 am, Jason Swails wrote:
> > > > On Thu, Oct 18, 2012 at 5:40 AM, Mu Xia <muxiachuixue.163.com>
> wrote:
> > > >
> > > >> Hi all,
> > > >>
> > > >>
> > > >> I want to get an average structure of the ligand-protein complex
> from
> > > >> the
> > > >> trajectories generated by MD. So I use the ptraj command. The input
> > file
> > > >> is
> > > >> as following.
> > > >>
> > > >>
> > > >> trajin production1.mdcrd
> > > >> rms first mass .CA,C,N
> > > >> average a.pdb pdb
> > > >>
> > > >>
> > > >> When examining a.pdb in VMD, I find that the X-H (X is the heavy
> atom)
> > > >> bonds are abnormally short.
> > > >>
> > > >
> > > > This makes sense. H atoms typically rotate fairly freely (they are
> > small
> > > > and there is little steric hindrance in many instances to free
> > rotation).
> > > > Also, for groups like CH3, the 3 hydrogens are, at least
> approximately,
> > > > rotationally degenerate, meaning they should have approximately the
> > same
> > > > average location (which will be nearly on top of the heteroatom).
> > > >
> > > >
> > > >> My question is, how could I get a correct average structure
> containing
> > > >> normal bonds and coordinates?
> > > >>
> > > >
> > > > What you got *is* a correct average structure (i.e., it is *the*
> > average
> > > > structure). "Normal bonds and coordinates" would be something you
> > would
> > > > find in a 'representative structure' in cluster analysis or something
> > of
> > > > the like.
> > > >
> > > > HTH,
> > > > Jason
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > Dr. Thomas Steinbrecher
> > > formerly at the
> > > BioMaps Institute
> > > Rutgers University
> > > 610 Taylor Rd.
> > > Piscataway, NJ 08854
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> > >
> > _______________________________________________
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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 Thu Oct 18 2012 - 08:00:04 PDT
