AMBER: Thermodynamic Integration for conformational changes?

From: Grzegorz Jezierski <>
Date: Tue, 26 Jul 2005 19:33:00 +0200

Dear AMBER users,
We are interested in the free energy change upon a rather complicated
conformational change of the system, which involves several structural
parameters like bonds, angles and dihedrals. We would like to avoid the
use of umbrella sampling techniques, if possible.
Is it possible to estimate this free energy change with Thermodynamic
Integration within Amber 8, i.e. to define the perturbation in terms of
change of dihedral angles, angles and bonds? In the tutorials and
manual only the perturbation of atom types, charges is illustrated.
Unfortunately, we could not find similar examples with the perturbation
of dihedrals, bonds and angles to establish topology perturbation file
in Amber 8 . To our knowledge this was possible in the old Gibbs module
of Amber 6. In this outdated version one could specify the initial and
the final values of the structural parameters in the input command file
Can one perform the same using TI method in Amber 8?
Thank you in advance,

G. Jezierski
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Received on Tue Jul 26 2005 - 18:53:00 PDT
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