Date: Sun, 19 May 2013 14:38:08 +0530
Dear Sir,
i am trying to use grid command for calculating water and ion density in RNA.
I followed your instruction given in amber forum. The ouput is given
below. i have some unusual density seen along the side wall of the
box. pls suggests.?
http://archive.ambermd.org/201005/0791.html
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
trajin traj.1
trajin traj.2
trajin traj.3
trajin traj.4
trajin traj.5
trajin traj.6
trajin traj.7
trajin traj.8 1 3000 1
center :1-12 mass origin
image origin center
center :1-24 mass origin
image origin center familiar
rms first mass out rms-grid :4-9,16-21
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 :1-24
--tec3
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(image/png attachment: RNA_wat_denisty.png)
