[AMBER] Calculate water density in the protein water channel by Amber 16

From: ūh <zhangyue16.mails.jlu.edu.cn>
Date: Mon, 26 Mar 2018 21:20:26 +0800(CST)

   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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 26 2018 - 06:30:03 PDT
Custom Search