I used MMPBSA.py to calculate deltaG of binding of protein-ligand complex after 10ns MD simulation.
The result is shown in the following line
DELTA G binding = -35.5263 +/- 2.7449 0.1228
I then performed per-residue decomposition on the same trajectory and topology files and got the following result
DELTA G binding = -37.4528 +/- 2.6611 0.1190
The discrepancy in the Poisson Boltzmann calculation was not significant (see below)
DELTA G binding = -29.2195 +/- 3.2998 0.1476
DELTA G binding = -28.9779 +/- 3.2726 0.1464
I'm using Amber11 and AmberTools 1.5
Any suggestions regarding the discrepancy observed in the GB calculation would be most welcome
Regards
Geroge
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 09 2012 - 04:30:02 PDT
