VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 19 2004 - 07:54:36 CST

Dear Han,
  How did you "move" the ligand? Did you do it with the
Mouse->Move functions in the GUI, or with one of the several
transformation subcommands of the 'atomselect' command?

If you did it by loading them as separate molecules and toggling one
of them "fixed" then translating and "unfixing", that would explain the
behavior you're seeing. You want to use one of the first two methods
I mention above.

Let us know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu
 

On Mon, Jan 19, 2004 at 09:03:48PM +0900, Han Choe wrote:
> Hi everyone,
>
> It's very difficult for me to dock a ligand to a receptor in VMD. After
> I move a ligand to a receptor's binding pocket, a rotation takes two
> molecules apart. It looks like the two molecules have different origins
> of rotation. Is there an easy way to solve this problem?
>
> Cheers,
> Han 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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