Hi,
Not sure this is exactly what you're looking for, but you might want
to check out the 'watershell' command, which will record the number of
water molecules in the 1st and 2nd solvation shells defined by a lower
cutoff (default 3.4 Ang.) and an upper cutoff (5.0 Ang). This will
produce a file containing Frame number, # lower, and # upper. You
could then calculate a histogram which shows where each value peaks
and use a second run with the 'closest' command to generate
trajectories containing the first and second or just the first
solvation shells for further calculation/visualization etc. For
example:
parm myparm.parm7
trajin mycrd.nc
watershell :MOL W1.dat W1 lower 3.0 upper 5.0
multihist W1[*] out W1.hist.agr bins 50
Hope this helps,
-Dan
On Tue, Feb 3, 2015 at 8:54 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Dear Amber users!
>
> I'm looking for the possibility to calculate number of the water molecules
> detected within the protein (here I define area of interests as :MOL)
> during molecular dynamic simulation. As the result it will be better to
> obtain some graph as well showing dependence of the water within 3 A of Mol
> on Y and time on X. Some time ago I did it using some vmd script which was
> lost :) so not I'm looking for another possibility to do this kind of
> analysis using cpptraj.
>
> I'd be thankful for any help,
>
> James
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Tue Feb 03 2015 - 08:30:03 PST
