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
Received on Wed Jun 06 2001 - 14:14:10 PDT
