AMBER: Linear Interaction Energy

From: Daniel Oehme <>
Date: Wed, 21 Sep 2005 11:39:53 +1000 (EST)

Dear AMBER users,

I am currently trying to do Linear Interaction Energy
calculations on HIV Protease complexes using the
methodology defined by M.M.H van Lipzig et al (2004)
using AMBER8.0. After running an MD simulation they
calculate the interaction energy between a ligand and
its surroundings by calculating the average difference
in energy between the total system and the different
components that make up the system. That is the
solvent, the receptor and the ligand. The energies of
each component are calculated by single-step energy

The problem I am having is that to do these single
step calculations, I will need parameter and
coordinate files for the different components. The
coordinate files are easily created, as are the
parameter files for the ligand and the receptor,
however I am not sure how, or if it is even possible,
to create a parameter file for the solvent.

Does anybody know of any way in which I can create
this parameter file or does anybody have any other
ideas on how to use AMBER8.0 to calculate Linear
Interaction Energies?


Daniel Oehme

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Received on Wed Sep 21 2005 - 02:53:00 PDT
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