Thanks for pointing this out. I saw there's GIST command that calculates
several solute-water quantities as well as the density on the grid :)
On Mon, Feb 9, 2015 at 4:25 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Feb 9, 2015 at 3:40 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
>
> > Dear AMBER experts,
> >
> > >From what I understand, ptraj or cpptraj cannot identify buried water or
> > buried water clusters. Am I wrong?
>
>
> How do you define a "buried water cluster"? You can compute water
> densities using the "grid" or "volmap" commands in cpptraj. Then you could
> post-process that grid and pull out voxels that have a density
> significantly higher than bulk water. Then of course you need to define
> "buried", but if you have a way to assign voxels as either buried or not,
> then it's pretty easy to filter out "buried" voxels with higher-than-bulk
> water densities. This doesn't really work for a single frame, though. You
> would need to take the density grid averaged over the whole trajectory and
> extract the water molecules near the high-density voxel in each frame
> (which actually sounds a bit like what the "spam" action in cpptraj does).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 09 2015 - 15:00:02 PST
