Hi,
If your channel is aligned along one of the x, y, or z axes you may
have some success using the 'density' command in cpptraj. See the
manual for full details.
-Dan
On Mon, Mar 26, 2018 at 9:20 AM, 张玥 <zhangyue16.mails.jlu.edu.cn> wrote:
>
> Dear Sir
>
> I have calculated water density in the protein water channel by Amber 16 and
> got a wat.grid file. Here is my input file water-density.in.
>
> trajin BM2-1_image-2.nc
>
> center :1-33 mass origin
> image origin center
> center :1-132 mass origin
> image origin center familiar
>
> rms first mass out rms-grid :1-132
> grid wat.grid 100 0.5 100 0.5 100 0.5 :WAT.O
> grid na.grid 100 0.5 100 0.5 100 0.5 :Na+
> grid cl.grid 100 0.5 100 0.5 100 0.5 :Cl-
>
> translate x -0.25 y -0.25 z -0.25
>
> average avg.pdb pdb :1-132
>
> After that, I got some files (including rms-grid, avg.pdb, cl.grid, na.grid
> and wat.grid). I started up Chimera, load up avg.pdb, and load up the
> wat.grid. I got a figure which shows the water in the channel.
>
> However, for the following analysis, I really want to know the certain
> values of water density along the protein water channel. How should I do to
> get certain values about water density?
>
> All the files were listed in appendix.
>
>
> Sincerely yours,
>
> Yue Zhang
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 10 2018 - 07:00:03 PDT
