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
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Received on Mon Feb 09 2015 - 13:30:02 PST
