one could do that, but most clustering algorithms have a built-in method for
selecting the "representative" structure for the cluster.
On Wed, Nov 18, 2009 at 10:32 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> So I get the conformations clustered and then just select for example the
> conformations in each cluster with lowest energy, right?
>
> Best regards,
> Andrey
>
> 18.11.09, 08:53, "Carlos Simmerling" <carlos.simmerling.gmail.com>:
>
> > the ptraj program that Andrew asked about also supports clustering, so if
> he
> > already knows how to use ptraj there's no reason to learn MMTSB.
> > On Wed, Nov 18, 2009 at 8:39 AM, Renata KWIECIEN <
> > Renata.Kwiecien.univ-nantes.fr> wrote:
> > > Check "cluster" option in MMTSB.
> > > http://blue11.bch.msu.edu/mmtsb/Main_Page
> > >
> > > Best regards,
> > > Renata
> > >
> > > > Actually the question is about how to generate protein conformations
> > > > ensemble and then to select the most probable conformations.
> > > > It s possible to generate receptors ensemble using namd and it should
> be
> > > > possible by using amber, but I need let s say 30 most probable
> > > > conformations of proteins which have the highest occurence rate in
> the
> > > > 5-10 nanosecond trajectory.
> > > >
> > > > Is it possible to do it by ptraj for example?
> > > >
> > > > Best regards,
> > > > Andrew
> > > >
> > > > 12.11.09, 08:30, "Adrian Roitberg" :
> > > >
> > > >> I am not sure, but I believe that Andy Mc Cammon's group has
> implemented
> > > >> this setup in their own web site, extending it from namd as in the
> paper
> > > >> you mentioned, to amber now.
> > > >> Adrian
> > > >> Andrew Voronkov wrote:
> > > >> > Dear Amber users,
> > > >> > are there any tutorials online on usage of some analogs of relaxed
> > > >> complex scheme, described here:
> > > >> >
> > >
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516539/?tool=pubmed#aff-info
> > > >> >
> > > >> > I mean optimization of MD trajectory snapshots and usage of most
> > > >> probable protein conformations from MD trajectories in Amber?
> > > >> >
> > > >> >
> > > >> > Best regards,
> > > >> > Andrey
> > > >> >
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Received on Wed Nov 18 2009 - 09:30:04 PST
