VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 12 2009 - 14:59:04 CDT

Hi,
  Are you moving the atom coordinates manually using the
Mouse->Move->Molecule menu, or are you using atom selections for this
purpose?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 12, 2009 at 03:48:23PM -0400, Steve Seibold wrote:
> I have constructed a pdb model of a compound and am trying to place it in
> my protein. When I do this I open up both protein pdb and my compound pdb
> simultaneous in VMD. The problem is when I try to position the compound
> into the pocket of the protein. I cannot seem to move it closer in the
> sense that no matter how long I freeze the protein and move the compound
> it never appears to get closer. Is this just because it is VERY difficult
> or is there some barrier to doing this. I attempted it for quite some time
> and could never get the compound positioned correctly. Is there a way to
> do this with VMD. I am using the WINDOW version.
>
>
>
> Thanks, Steve
>
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078