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?
Thanks
On Mon, Sep 23, 2013 at 12:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Sep 22, 2013 at 9:46 AM, Subrata Paul <paul.subrata34.gmail.com
> >wrote:
>
> > Is it possible to water cluster in amber12. ?
> >
> > if possible, How ?
> >
>
> It's not clear what exactly you want. You can use the "grid" or "volmap"
> commands in cpptraj to compute water densities on a grid (the former is a
> simple histogram, the latter is like the 'volmap' routine in VMD). You can
> figure out where water tends to 'cluster' this way, although this is
> difficult to do unless the solute is held fairly rigid.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 23 2013 - 14:00:06 PDT
