AMBER Archive (2006)

Subject: Re: AMBER: Grid command of ptraj

From: Sean Rathlef (
Date: Sat Oct 14 2006 - 05:25:59 CDT

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 ...

  ----- Original Message -----
  From: Atsutoshi Okabe
  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


  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?




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