Re: AMBER: Thermodynamic Integration for conformational changes?

From: Carlos Simmerling <>
Date: Tue, 26 Jul 2005 14:02:57 -0400

I don't know a good solution for doing such a complicated change with TI,
there are so many changes and any part along the way will affect the overall
free energy difference. It might be much safer to use MM-PBSA
to get an estimate of the difference since it relies only on the endpoints,
not good sampling all along the path.

Grzegorz Jezierski wrote:

> 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 In this outdated version one could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 explicitly.
> 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 - 19:53:00 PDT
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