AMBER Archive (2006)

Subject: Re: AMBER: MM_PBSA

From: Thomas Steinbrecher (
Date: Thu Nov 16 2006 - 10:21:55 CST

Dear Varsha,

> I never added any solvent cap while creating topology
> file --> Can i still use PB to calculate binding
> energy.
> I used periodic boundary conditions for MD --> whihc
> turns off Generalized Born --> can I still calculate
> binding energy using PB=1 in MM_PBSA.

the typical thing for MM-PBSA is an MD run with explicit solvent followed
by an MM-PBSA evaluation using the PB-solvent model. Nothing
stops you from instead combining implicit solvent MD runs with MMPBSA or

However, the bigger the differences between your simulation and evaluation
sovent models are, the more likely you will get bad results in my opinion.
I would normally assume explicit solvent and PB to be more 'exact'
solvent descriptions than GB, but that doesn't mean they give correct
answers in MMPBSA all the time.

You should set up a test case for your system in which you can compare
MMPBSA results with experimental data, to see which solvent model is



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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