Re: MMPBSA calculation using NAMD

From: Aron Broom (
Date: Sun Sep 15 2013 - 17:49:19 CDT

Some of the better put together MMPBSA tools are included in the free
AMBERTools package. MMPBSA and MMGBSA are post-processing methods, so you
can run the simulation in NAMD, save the DCD output reasonably often, and
then do the analysis in AMBERTools, provided you are careful about setting
the parameters to match what NAMD would have used during the simulation.


On Wed, Sep 11, 2013 at 8:37 AM, sudipta <> wrote:

> Hi All,
> Can anyone give some suggestions how do I perform MMPBSA calculation in
> combination with alanine scanning using NAMD?
> Best
> Sudipta

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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