AMBER Archive (2009)

Subject: Re: [AMBER] MD snapshots of most probable protein conformations in Amber

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Wed Nov 18 2009 - 09:32:11 CST

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_at_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_at_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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