AMBER Archive (2005)

Subject: Re: AMBER: Thermodynamic Integration for conformational changes?

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 26 2005 - 13:42:54 CDT

On Tue, Jul 26, 2005, Grzegorz Jezierski wrote:

> 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 In this outdated version one could specify the initial and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.

You are correct: there is no way with the current thermodynamic integration
code to look at conformational changes; we indeed recommend umbrella sampling
for such investigations.

...dac

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