Re: [AMBER] water cluster analysis

From: Jason Swails <>
Date: Mon, 23 Sep 2013 17:51:04 -0400

On Mon, Sep 23, 2013 at 4:48 PM, George Green <> wrote:

> What you describe would be very useful for me too. If you have time, could
> you please elaborate on how the solute should be held? Is it a RMS fitting
> procedure?

No, not really. What I meant was to hold the solute fixed via positional
restraints in the MD. If you've already run your system without restraints
on (at least the backbone, but probably all heavy atoms), then extracting
water densities will be more challenging.

The main problem is that the grid is defined in cartesian space. Typically
you want the water density either around the surface of the solute (the
solvation shell) or in some pockets where the water molecules behaves quite
differently from bulk water. The problem with evaluating this on a grid is
that the solute can move, meaning that the solvation shell moves around on
the grid from frame to frame.

This can be alleviated to some degree by RMS-fitting the solute (re-imaging
is also recommended), but even this fitting does not eliminate protein
breathing and other, non-translational and non-rotational motions of the
molecule. If you need your solute to be flexible, then the only real
places you can look for water density using either of these grid-based
methods is in well-conserved pockets. In this case, you want to do some
careful RMS fitting (you need to play around with the part that you fit to
make sure that the water pocket is always in the same place on the grid,
and always image the solvent around that point). In general you will have
to evaluate each pocket separately (since you can't assume that the water
pockets will be in the same place on the grid relative to each other in
every frame).

If you simply restrain your solute heavy atoms to the same small region of
space, then it is very easy to define a grid around the solute that is
effectively the same for every snapshot (since the solute atoms are barely
moving). Many grid-based water profiling techniques (e.g., GIST [<>],
WaterMap [], 3D-RISM, and szmap [] to name a few) consider a rigid solute for
this reason.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 23 2013 - 15:00:03 PDT
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