AMBER Archive (2006)

Subject: AMBER: Grid command of ptraj

From: Atsutoshi Okabe (
Date: Sat Oct 14 2006 - 02:31:01 CDT

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


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?







  • application/octet-stream attachment: wat.rar


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