AMBER Archive (2002)

Subject: Re: LEAP - Introducing dummy atoms

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Mon Dec 02 2002 - 13:11:27 CST

Does this ONLY happen when/after you have introduced a dummy
atom? Does Leap work OK when you simply setup the cyclodextrin,
view it and then save the topology/coordinate files?

jim

On Mon, 2 Dec 2002, Miguel de Federico wrote:

> I want to put a dummy atom in the center of a macrocycle (alpha -
>cyclodextrin). I started editing my unit for the cyclodextrin with xLEaP
>and adding one atom by usin "draw" This dummy atom is not bonded to any
>other, but is put for managing better with some restraints. After it I
>used "edit selected atoms" and changed the type of the new atom to dummy
>atom. It seems to work, but when I save it as topology and coordinate
>files, I have found that the structure created (cyclodextrin + dummy) is
>bidimensional, with all atoms in a plane.
>
> After this I tried to create a new unit with just a dummy atom in it,
>and combining it with the previous cyclodextrin unit. Other time, the
>structure seems correct with xLEaP, but the structure created is
>bidimensional.
>
> I seems incredible, but this is what I found... Could anybody tell me
>how to introduce a dummy atom in my cyclodextrin?
>
> Thank you,
>
>Miguel.
> 

-- 

----------------------------------------------------------------------------
James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue                      
University of California                  
San Francisco, CA 94143-0446               
----------------------------------------------------------------------------