AMBER Archive (2008)

Subject: RE: AMBER: Average structure

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Apr 22 2008 - 02:02:23 CDT

Hi:
I remember that Ross has already warned on several occasions against such a use of the average of the cartesian coordinates explored. I opted for the minimum structure, although this is also a complex affair when - as in my case - dealing with a protein-ligand complex in a lipidic membrane.
Cheers
francesco pietra

--- On Mon, 4/21/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: Average structure
> To: amber_at_scripps.edu
> Date: Monday, April 21, 2008, 7:27 PM
> Hi James,
>
> I would also like to point out that if by average structure
> you just mean
> the average of the cartesian coordinates explored then you
> should think very
> carefully about what this actually means and whether it is
> at all useful.
>
> E.g. consider a freely rotating methyl group:
> H
> /
> C--H
> \
> H
>
> Then think about what the average structure for this would
> be. It is
> effectively:
>
> C--H3
>
> I.e. all 3 protons sitting on top of each other along the
> vector that forms
> the center of rotation - so not really that interesting.
> Much more
> interesting is to do some kind of cluster type analysis or
> something that
> plots say a color plot of RMSD from a given representative
> structure.
>
> See the following tutorial:
> http://www.ambermd.org/tutorials/basic/tutorial3/index.htm
> which goes over
> average structures and then more advanced analysis
> techniques.
>
> Good luck,
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
> Note: Electronic Mail is not secure, has no guarantee of
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> be read every day, and should not be used for urgent or
> sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of David
> Cerutti
> > Sent: Monday, April 21, 2008 09:13
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Average structure
> >
> > Hi James,
> >
> > The average structure from a given length of
> simulation
> > is only that.
> > 10s is not a long trajectory by current standards, but
> it's
> > not terribly
> > short either. If you're interested in an average
> structure,
> > it should be
> > the average structure for whatever length of
> trajectory you
> > have, less
> > some portion at the start of the run which you'll
> discard for
> > "equilibration" (I use the quotes because
> there can be many
> > definitions of
> > qhat it means to be equilibrated, some of them more
> difficult
> > to satisfy
> > than others).
> >
> > It is conceivable to me that you might observe all
> of the
> > different
> > motions that you're going to see from this protein
> in the
> > space of 10ns,
> > just not in all possible combinations (maybe you see
> loop A
> > flips out and
> > back, loop B could curl up, and loop C twists or turns
> into a
> > helix, but
> > observing all of these different motions in every
> possible
> > combination
> > would take a long time). It may be helpful to
> determine if
> > there is a
> > significant "core" to the protein that
> remains very stable
> > and can thus be
> > used to align the trajectory, then construct some sort
> of
> > library of all
> > the loop motions that you see, and use the point at
> which
> > your library is
> > no longer growing as a metric for
> "convergent" behavior. I'm
> > not sure how
> > to do this conveniently in AMBER, though; I'm
> thinking of
> > writing my own
> > program for this type of analysis.
> >
> > The average structure can also serve as your basis
> for
> > aligning the
> > trajectory, but I like to first look for any parts of
> the
> > protein that
> > move very little so you reference point corresponds to
>
> > something that is
> > easily recognizable, which the average structure may
> not be.
> >
> > To remove the overall translation and rotation,
> you just
> > align to some
> > structure (it can be one frame of the trajectory, but
> in this
> > case the
> > average structure is often preferred). Again, if you
> can
> > find some very
> > stable residues in the central regions of your
> protein,
> > aligning to those
> > (or, the average conformation of those particular
> residues)
> > might be a
> > more intuitive way to look at the protein motions.
> >
> > Dave
> >
> > On Mon, 21 Apr 2008, James Thomas wrote:
> >
> > > Dear Amber Community
> > >
> > > I would like to inquire if average structure of
> MD run,
> > after 10 ns for a
> > > protein of ~100aa is reliable as a starting point
> for
> > further analysis?
> > > I heard from a post-doc who is experienced in
> Amber, that
> > average structure
> > > is not reliable for short duration simulation.
> > > I look forward to your comments / advices.
> > >
> > > How to remove the overall translational &
> rotational motion
> > in Amber9
> > > trajectories?
> > >
> > > Many thanks.
> > >
> >
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