RE: AMBER: Amber 8: questions about free energy perturbation

From: Angela Liu <>
Date: Mon, 12 Sep 2005 03:37:30 -0700 (PDT)

Dear Prof. Case.

I am sorry that I didn't make myself clearer, in
Kollman's 1993 review on Chem. Rev., he illustrated
that mutating a THY to an ADE (pyrimidine to purine)
causes some non-bonded terms to be missed in the
calculation (such as the methyl-hydrogen H5 and C6's
hydrogen H6 in THY on page 2399 of the review),
because these atoms were directly bonded in the
"single topology".

I have read and understood your tutorial of mutating
toluene to nothing. However, in the Amber 8 manual, it
specifies that dummy atoms can only exist in the
perturbed Hamiltonian on Page 134 of Section 5.13:

"Eq. (5) is designed for having dummy atoms in the
perturbed Hamiltonian, and "real" atoms in the regular
Hamiltonian. You must ensure that this is the case
when you set up the system in LEaP. There is currently
no facility to have dummy atoms in both V0 and in V1."

This means that if the starting geometry and the final
geometry both have exclusive atoms to themselves, the
"single topology" will not be able to describe them
both. This is the case for mutation of say ADE to GUA
(ADE has an amino group at C6 position, and GUA has an
amino group at C2 position, thus requiring dummy atoms
in both ADE and GUA).

So what is your suggested work-around for such
situations? Thank you very much for your time and


--- case <> wrote:

> >So if I DO want to calculate the free energy of a
> >mutation, say from purine to pyrimidine (a problem
> >clearly explained in Kollman's 1993 review with
> >"single topology")
> Sure, since we do use a "single topology" approach.
> There is a tutorial on
> changing toluene to nothing, which is not
> conceptually different from changing
> a purine to a pyrimidine.

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Received on Mon Sep 12 2005 - 11:53:00 PDT
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