AMBER Archive (2001)

Subject: question

From: Zhangxd (zhangxd_at_alien.biochem.wfubmc.edu)
Date: Thu Jul 19 2001 - 09:05:18 CDT

hi, everyone

Now I face one question about the free energy. After docking with
autodock3.0 program, two ligand configurations (A,B)were taken, then MD
was taken place with AMBER6.0 for two complexes AC and BC, protein C
and Ligands A and B. When MM_PBSA was performed, the interesting thing
appared (the change of entropy was not considered).

(1) With different traj for complexes AC and BC, protein C and ligands A
and B,

G(AC-A-C)-G(BC-B-C)>0,

where G(AC-A-C)=G(AC)-G(A)-G(C) with MM_PBSA module,

(2) When the same traj was used, i.e. only the traj of complex was used,
the results was that

G(AC-A-C)-G(BC-B-C)<0,

which was agreement with Docking results.

Thank you very much for your suggestions,

With best regards,
Xiaodong