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 - 07:09:52 CST
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?
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.
> 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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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