AMBER Archive (2002)

Subject: LEAP - Introducing dummy atoms

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Mon Dec 02 2002 - 10:42:49 CST

 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.