AMBER Archive (2006)

Subject: Re: AMBER: Calculate interaction energy between small organic molecules

From: David A. Case (
Date: Tue Aug 22 2006 - 01:14:15 CDT

On Mon, Aug 21, 2006, Björn C-G. Karlsson wrote:
> Now my question is: I know that it is possible to extract energy information
> from a simulation such as Etot, Epot and Ektot using a script, but is it
> possible to calculate the non-bonded interactions for single molecules
> during a simulation plotting these values and so to speak get a rough
> measurement on the binding energy when the molecule interacts with another
> molecules and experiences a decrease in Epot?

There are some decomposition options in mm_pbsa that may be of interest.
You would probably treat the solute as a "ligand" and the solvent as the
"receptor". As others have noted, however, this sort of analysis may miss
important features -- it was designed for "receptors" with well-defined
structures, not really for solvents.

...good luck...dac

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