Thank you sir
On 7/3/14, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>> >
>> _______________________________________________
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>>
>
>
>
> --
> -------------------------
> 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
>
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Received on Wed Jul 02 2014 - 22:00:02 PDT
