AMBER Archive (2001)

Subject: LIE method

From: Katherine Wallis Abold (kabold_at_umich.edu)
Date: Wed Jun 06 2001 - 16:14:10 CDT

I am using Sander_classic to run MD calculations to obtain binding
energies. To do this I need to breakdown the energies obtained from the
dynamics simulation to get the eletrostatic and van der Walls interaction
energies between ligand and its surroundings. (Methodology based on
PROTEINS: Structure, Function, and Genetics 34:69-81 (1999) - a method
designed to estimate binding free energy).

In the gibbs program there is a IPERAT command in the namelist &cntrl
which I believe can breakdown the energies.

There is no command that I can find in either sander program. Can anyone
tell me how to do this?

Thanks in advance,

Katherine W. Abold
Graduate Student in Medicinal Chemistry
University of Michigan