Re: [AMBER] rdf or watershell

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 1 Jun 2016 08:47:45 -0600

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
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