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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Received on Mon Mar 26 2018 - 06:30:03 PDT
