AMBER: General Question about AMBER's Free Energy Perturbation Method

From: Ilyas Yildirim <>
Date: Wed, 15 Dec 2004 23:13:07 -0500 (EST)

 Dear AMBER Users and Developers,

 I have a general question about AMBER's FEP calculation. I want to make a
small change on a nucleic acid, and do a FEP calculation from the
original structure to the newly created structure. In the 'Crown ether in
vacuum' tutorial, the perturbation is done by using GIBBS. In the initial
system, there is a Na+ ion, and it is perturbed from Na+ to K+ (and then
from K+ to Cs+ ion). In this tutorial, 1 atom is changed to another atom.

 My question is as following: Let's say that I have an organic molecule,
like Guanine, and want to change the amino group (-NH2) to a carbonyl
group (-O) (Or vice verse). [NH2 -> O or O -> CH2] How can this be
specified in xleap? Or should I do a [N -> O] or [O -> N] perturbation,
and then include the hydrogen atoms?

 From GIBBS and XLEAP's interface, I realized that only 1 atom can be
perturbed. Therefore, I wonder if it is possible to do a
perturbation like NH2 -> O in AMBER 8. Thanks in advance.

  Ilyas Yildirim
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  -                     -
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Dec 16 2004 - 04:53:00 PST
Custom Search