Subject: moving molecules

From: Alice NgarKit Ko <[email-masked]>
Date: Thu, 23 Aug 2001 14:46:28 -0500 (EST)

Hi all,

Does anyone know how to move molecules around?  I want to move some water
molecules in some specific area inside my protein.  But I don't know the
xyz coordinates of the target locations.  I would like to be able to
visualize the protein and the water molecules, and then just use the mouse
to drag the water molecules into my protein.  Is there any software out
there can do that?  I would appreciate any suggestion.

Thank you very much

Alice

---

From: Barry Isralewitz <[email-masked]>
Date: Thu, 23 Aug 2001 16:30:28 -0500

Hi,

> there can do that?  I would appreciate any suggestion.

	The molecular visualization program VMD offers a couple of
ways to do this.  You can simply move static molecules, or get as
fancy as real-time interactive force-feedback molecular dynamics (when
connected to the parallel MD program NAMD).

	VMD is released by the Theoretical Biophysics Group, at the
University of Illinois at Urbana-Champaign.  VMD is free academic
software, download it at:

http://www.ks.uiuc.edu/Research/vmd/

	The easiest way to move molecules is described in the online
documentation for VMD, see "Move Mode" in the "Mouse Form: Object
Menus" section.  After the move, just write out the new coordinates to
a .pdb file.

http://www.ks.uiuc.edu/Research/vmd/current/ug/node36.html#SECTION00742400000000000000

	(Obligatory bias admission: I do some programming for VMD nowadays.)

					Happy modeling,

					Barry

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: [email-masked]      http://www.ks.uiuc.edu/~barryi