AMBER Archive (2006)

Subject: RE: AMBER: Grid command of ptraj

From: Thomas Cheatham (
Date: Tue Oct 17 2006 - 10:40:22 CDT

> 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 ?

The grid ONLY contains the density for the atoms you selected. If you
want to display something else, you will have to load that up.

> > 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

To get a PDB file of residue one in the same reference frame:

trajin md.crd 1 1 1
trajout snap pdb
center :1
strip :2-99999999
translate x 0.25 y 0.25 z 0.25

(the grid runs from -49 to 50 so the coordinates need to be shifted by
+1/2 grid spacing or 0.25).

Then, load up the PDB file "snap.1" and then load up the grid in

Likely you will want an average structure (unless :1 is rigid) that you
can load up and RMS fit to the "snap.1".

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