Dear Atsutoshi,
I feel comfortable with this medium. These images of solvation are abstract, but this does not mean that ptraj is useless in this situation. I wouldn't use XPLOR unless it was not going to have to with charmm or related phenomenom. Yet as for the images you are choosing to regenerate, I suggest a reciprocal approach -- and that is harmony ...
smr
----- Original Message -----
From: Atsutoshi Okabe
To: amber.scripps.edu
Sent: Saturday, October 14, 2006 12:31 AM
Subject: AMBER: Grid command of ptraj
Dear all,
I want to visualize solvent distributions (i.e distributions of the first water shell) around one solute molecule.
So I executed the following grid command within ptraj
trajin md.crd
center :1
image
rms first mass out rms :1
grid wat.xplor 100 0.5 100 0.5 100 0.5 :WAT
Then I got the wat.xplor file and visualized the file with chimera soft ware. (attached files)
But I doubt that I could get the figure I would intend.
Actually I can't understand grid command and the ouput file( wat.xplor file )
I don't know how I should deside the value of grid point and grid space.
Could you give me any help?
Tnanks
Atsutoshi
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Received on Sun Oct 15 2006 - 06:07:16 PDT
