The 'watershell' command should do what you want, but you'll have to
adjust the cutoffs. The default behavior of 'watershell' is to count
number of waters in the first shell (< 3.4 Ang) and second shell (<
5.0 Ang). You'll have to adjust at least one of the cutoffs - probably
the 'upper' cutoff is easiest.
-Dan
On Tue, May 31, 2016 at 7:31 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi List,
>
> I want to calculate number of water molecules within 7 A from the ligand in
> the cavity and monitor the water occupancy from the trajectory. Should I
> use radial function or watershell should be sufficient for the analyses?
>
> Regards,
> Neha
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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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 Wed Jun 01 2016 - 08:00:05 PDT
