VMD-L Mailing List

From: Han Choe (hchoe_at_amc.seoul.kr)
Date: Tue Jan 20 2004 - 01:24:57 CST

Dear John,

Thanks a lot. You guessed correctly what I did. I'll do what you
suggested.

Cheers,
Han

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Monday, January 19, 2004 10:55 PM
To: Han Choe
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: docking in VMD

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 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
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