AMBER: some question about MM-PBSA

From: scopio <>
Date: Thu, 20 Jan 2005 23:10:39 +0800

Dear Amber users:

I'm currently learning MM-PBSA to calculate binding energy of my complex.
Although I've read the manual and some papers about mmpbsa, I still don't
fully understand it. I have some questions about it and hope you could
help me to understand it.
1). Should the trajectory used for MM-PBSA be equilibrated trajectory? For
example, when RMSD plot shows a 3ns MD simulation equilibrated/stabilized
 from 2ns to 3ns, should the trajectory which is used for MM-PBSA
generating snapshot be picked out from 2ns to 3ns?
2). If the system contains counterions, is it necessary to have
counterions included in the Receptor?
3). sometimes the absolute value of GBTOT is twice as that of PBTOT. I'm
wondering which method is more accurate.

It will be highly appreciated to get any helps from you! Thanks!

Best Regards!


JunJun Liu
College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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Received on Thu Jan 20 2005 - 15:53:00 PST
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