Re: [AMBER] grid analysis

From: Daniel Roe <>
Date: Wed, 2 Jul 2014 08:03:25 -0600


If your grid shows high density of water there, it means just that.
Remember that grids don't distinguish between waters, so you can't tell
from the grid whether that density is from a single water or from multiple
waters. You could look at solute-solvent hydrogen bonding with the 'hbond'
action in that specific region (the 'nointramol' keyword is probably useful
in this case), then run 'lifetime' analysis to determine residence times.

Hope this helps,


PS - Another way you could look at areas of high density with the 'grid'
command is to use the 'pdb <pdbout> max <fraction>' keywords to write a
pseudo-PDB of grid points with density greater than <fraction>.

On Tue, Jul 1, 2014 at 8:04 PM, Mary Varughese <> wrote:

> HI,
> In grid analysis using ptraj option grid,
> on visualization of the hydration pattern in vmd, on increasing the
> contouring level above 3 times bulk water density presence of hydration
> sites decreases,
> two hydration sites are observed in the minor groove of DNA on both sides
> of the bound ligand at that state. Does that signify something like a high
> residence hydration site near the ligand.
> I want to know how grid analysis can be usefully interpreted?
> thanking you
> Mary Varughese
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jul 02 2014 - 07:30:03 PDT
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