On Wed, Jul 2, 2014 at 12:19 PM, Mary Varughese <maryvj1985.gmail.com>
wrote:
>
>
> lifetime analysis? what is this one. I didn't understand.
>
The 'lifetime' analysis simply calculates statistics for when a hydrogen
bond is present, how long is it present on average and what is the maximum
length of time it is present. The command is described in the Amber14
manual in "28.12.11. lifetime".
>
> Also in hbond analysis involving solvent, if % occupied is 178. What does
> it means. Does it indicates presence of more than one water?
>
Yes, on average.
-Dan
>
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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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 - 12:30:03 PDT
