VMD-L Mailing List

From: Ф¸»¹ó (helitrope_at_163.com)
Date: Mon Sep 03 2012 - 08:51:01 CDT

Hi everyone,
Today i showed a guy the principle of MM-PBSA and he asked me a question. The question is whether the ligand is in its relaxed form?
I know the MM-PBSA calculates the binding energy using the structure from a MD simulation, and both the ligand and the protein are not in the relaxed form. So, how to answer the basic probelem.
Can anyone please give me some suggestions?
Best wishes
Xiao Fugui