Hi
If your grid shows high density of water there, it means just that.
To make this clear; when contour level is increased. isn't?
lifetime analysis? what is this one. I didn't understand.
Also in hbond analysis involving solvent, if % occupied is 178. What does
it means. Does it indicates presence of more than one water?
Thanking you
Mary Varughese
On Wed, Jul 2, 2014 at 7:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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,
>
> -Dan
>
> 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 <maryvj1985.gmail.com>
> 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
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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Received on Wed Jul 02 2014 - 11:30:02 PDT
