AMBER Archive (2006)

Subject: AMBER: GBSA EGB = NaN

From: William Lianhu Wei (
Date: Thu Aug 17 2006 - 21:30:50 CDT

Dear all,

I finished molecular dynamics simulation of my system about 3ns. From the
energy profile, the system reached equilibrium at about 1.5 ns. I was trying
to calculate the binding free energy. The trajectories I used was after
1.5ns. No matter which trajectory I used, I always got EGB=NaN (on Complex
and receptor), and the program stopped at statistical calculation. The VDW
contribution is okay. Does anyone meet this before, or give me any clue for
that. In 2004 archive, there is somebody asked this, but there was no reply
for this. Thanks in advance.


William Wei                      Tel: +1-416-946-7551   
Faculty of Pharmacy            Email:
University of Toronto       
19 Russell St.            
Toronto, Ontario          
M5S 2S2,Canada
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