AMBER Archive (2006)

Subject: RE: AMBER: Grid command of ptraj

From: Atsutoshi Okabe (
Date: Mon Oct 16 2006 - 04:26:55 CDT

Dear Thomas,

Thank you for your very kind response.
I could almost understand by your help.
And could you please give me one more suggestion?

In my figure which I attached in previous mail, there is no solute Molecule
(residue 1) . How can I also display the solute molecule in my Solvent
distribution figure at once ?


-----Original Message-----
From: Thomas Cheatham []
Sent: Sunday, October 15, 2006 12:51 AM
To: Atsutoshi Okabe
Subject: Re: AMBER: Grid command of ptraj

> I want to visualize solvent distributions (i.e distributions of the first
> water shell) around one solute molecule.
> 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

This is fine; note that you will be viewing density around residue 1 and
will need a corresponding PDB in the same reference frame to visualize
properly... Also, if this were a truncated octahedon, it would be wise to
image with the familiar option

center :1 mass origin
image origin familiar

> 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.

The picture looks fine, it is just that you are contouring at a level that
shows most of the grid elements as "filled". In chimera, there is a
separate window that opens that controls the contour level, you can slide
the bar such that only high levels of density are displayed.

[As an aside, I haven't quite figured out how the numbering works for the
contouring, i.e. the mapping between "density" in the grid and the numbers
reported by chimera, but sliding to the right means more occupied.]

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