AMBER Archive (2007)

Subject: AMBER: Thermodynamic Integration for conformational changes?

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Aug 21 2007 - 11:57:47 CDT

I have carried out QM-MM (AM1) simulations for different conformations of a
98-atoms non-polymeric neutral molecule (solute) in explicit solvents. Would
like to compare with DFTB, if I get a license for that.

It is unclear to me how to relate above results to conformational energies, in
particular how to deal with ESCF. The results seem to suggest that
perturbations by the solvent cancel out by comparing ESCF for the conformers,
though the theory behind has not been examined.

At any event, I would like to calculate free energy changes for this system.
The question whether thermodynamic integration is appropriate for complicated
conformational changes received authoritative NO at Amber8's time (archives)
and is probably to be extended to Amber9. Are umbrella sampling or MM_PBSA
potential solutions? The first one, from the manual, also seems unable to deal
with multiple dihedral changes from one conformation to the other one. What
about MM_PBSA? Is any example to which to refer for the evaluation of absolute
free energies in explicit solvent by MM_PBSA?

Thanks
francesco pietra

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