AMBER Archive (2004)

Subject: AMBER: a general question about the mmpbsa method

From: a b (
Date: Wed Apr 28 2004 - 22:51:00 CDT

Hi there,
i have read some papers about the mmpbsa method, and from what i understand (and forgive me if i'm wrong, because i'm pretty new to the field) the main idea of the mmpbsa approach is to use the trajectories from an MD simulation as a statistical "pool" from which we calculate average free energies (mm in vacuum, pb, sa ...). in that case , wouldn't it be better to generate the statistical "pool" of configurations using monte carlo , which is supposed to do much better sampling, and then calculate the average free energies?
if not please explain, i am very interested to read opinions.
(if possible, can someone give me references for such a hybrid mc/mm-pbsa work?)
thanks a lot,

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