AMBER Archive (2005)

Subject: AMBER: mm_pbsa example number 3

From: Thomas Whitington (thomas.whitington_at_adelaide.edu.au)
Date: Fri Sep 09 2005 - 03:14:19 CDT

Hi all,

I have a question regarding the mm_pbsa examples distributed with amber 8, and
in particular, the example of estimating binding free energy.
The general approach for estimating binding free energy is to obtain overall
energy estimates for the recetor, ligand and complex separately, and then to
subtract the ligand and receptor estimates from the complex estimate.

This approach seems to be taken in the mm_pbsa example (example 3). However, the
ligand, receptor, and complex snapshots (generated in example 1) that are
analysed during mm_pbsa energy estimation all come from the same trajectory file
(named md_traj_short.mdcrd). In contrast, shouldn't separate "production run"
trajectories be generated for the ligand and receptor, after separate
minimisation and equilibration of these entities?

I have assumed that this approach was taken in the example because it is not
intended to be a thorough example of binding free energy estimation. However, if
I have interpreted the example incorrectly I would like to know. Any comments
regarding this would be greatly appreciated.

Kind regards,
Tom Whitington
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