From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Oct 31 2011 - 11:54:43 CDT

Coordinates of an atom can be seen by pressing 0 then clicking on the
atom. Coordinates will be displayed in the terminal. Alternatively:

set sel [atomselect resname theResidueNameOfYourLigand]
$sel get {x y z}

To move your ligand, it may be simplest for you to create a
representation of the ligand using the Graphics > Representations tool,
then setting your mouse to move the representation by either pressing 9
or via the menu Mouse > Move > Rep. Then just click on any atom in the
new representation of the ligand and drag to a new position.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Steven Neumann <s.neumann08_at_gmail.com> writes:
> Date: Mon, 31 Oct 2011 15:46:07 +0000
> From: Steven Neumann <s.neumann08_at_gmail.com>
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: move ligand around the protin
> 
> Dear VMD Users,
> 
> I am new in VMD software. I would like to run 10 simulations with my ligand
> in different orientations. My pdb file consists of protein and ligand. I
> would like to change the posiion of ligand around my protein:
> 1) How to show the coordinates in my display?
> 2) How to move ligand observing it on my display in order to save it then?
> (I know how to do it manually but I would like to see it)
> 
> Thank you,
> 
> Steven