Re: [AMBER] water cluster analysis

From: George Green <>
Date: Tue, 24 Sep 2013 00:57:41 +0100

Thanks very much for the detailed explanation. It has given me a good idea
on how to proceed. :)

On Mon, Sep 23, 2013 at 10:51 PM, Jason Swails <>wrote:

> 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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Sep 23 2013 - 17:00:04 PDT
Custom Search