AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Nov 18 2009 - 07:53:14 CST

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" <roitberg_at_qtp.ufl.edu>:
> >
> >> 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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> >> >
> >
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>
>
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