Re: AMBER: mm_pbsa example number 3

From: Carlos Simmerling <>
Date: Fri, 09 Sep 2005 07:19:59 -0400

In principle, yes. In practice, it has been reported that the
data can be more reliable if this is not done. Check some of the
published M-PBSA applications; both approaches have been
used. The basic issue is that the separate simulations may be poorly
converged, and that using the complex trajectory is approximate but
may be better converged (particularly if there is a receptor or ligand
conformational change on binding). If one wants relative binding
energies, the receptor ones cancel anyway.

Thomas Whitington wrote:

>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
>The AMBER Mail Reflector
>To post, send mail to
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Carlos L. Simmerling, Ph.D.
Associate Professor           Phone: (631) 632-1336
Center for Structural Biology Fax:   (631) 632-1555
Stony Brook University        Web:
Stony Brook, NY 11794-5115    E-mail:
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Received on Fri Sep 09 2005 - 12:53:01 PDT
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