AMBER Archive (2006)

Subject: AMBER: Grid command of ptraj

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
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

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

 

 

 


  • application/octet-stream attachment: wat.rar

image.jpg

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