The best way without modifying Sander is to postprocess your MD
trajectory. You can use Carnal and Anal modules to calculate the vdw and
ele energies between ligand and its enviroments. It means you have to
define the Group 1 as ligand and Group 2 as its enviroments (part of
protein or water).
If you want to calculate absolute binding free energy, LIE method is a
good choice. But if you only care about relative binding free energy
between ligands, MMPBSA method is a better choice.
Hope this helps.
Wei Wang
On Wed, 6 Jun 2001, Katherine Wallis Abold wrote:
> 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 - 20:24:26 PDT
