AMBER Archive (2008)

Subject: Re: AMBER: Average structure

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Mon Apr 21 2008 - 11:12:30 CDT

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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