AMBER: Amber 8: questions about free energy perturbation

From: Angela Liu <>
Date: Sun, 11 Sep 2005 17:43:41 -0700 (PDT)

Dear Amber developers and users,

I am learning how to use sander to carry out free
energy perturbation calculations and here are my three

1) In the older version of Amber (such as Amber 7 and
Amber 6), "gibbs" was the routine that is used to
calculate free energy perturbations. It uses "dual
topology" so that the unperturbed and perturbed
systems can have unique atoms to themselves. Kollman
indicated in his 1993 Chem Rev review that dual
topology methods often suffer from poor convergence
problems. Is this the reason why this "dual topology"
approach was no longer supported in Amber?

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"), is there no way Amber 8 can allow
this to be done?

2) As Pearlman and Kollman pointed out in "The
overlooked bond stretching contribution in free energy
perturbation calculations", J. Chem. Phys. 1991,
94:4532, for certain systems, bond stretching terms
are important to consider when calculating the free
energy. So in "gibbs", was the Hamiltonian expressed
according to intermediate bond stretching force
constant and equilibrium length (according to lambda
values), such as in

U_bond = [ (1-lambda) K_A + lambda K_B ] { R_AB - [
(1-lambda) R_A + lambda R_B ] }^2
where K_A, K_B, R_A, and R_B are the force field
parameters for the reactant A and product B?

Were the bond angles and torsional angles expressed
using similar equations, so that their contributions
to the free energy can be accounted for in "gibbs"?
>From the documentation of the source files in
$AMBERHOME/src/gibbs/, it seems to me that these are

3) How can I get hold of the source code of "gibbs" in
Amber 7 or 6? I tried "make" in the
$AMBERHOME/src/gibbs/ directory, but there were
problems with the Ewald routine (RE erfcfun) that
caused the "make" to fail. I wasn't sure how this can
be corrected.

Thank you very much for your time, suggestions, and

Best wishes,
Angela Liu

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Received on Mon Sep 12 2005 - 01:53:00 PDT
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