Re: AMBER: mm_pbsa example number 3

From: Thomas Whitington <>
Date: Sun, 11 Sep 2005 12:02:58 +0930

Hi Carlos,

Thankyou very much for your fast reply, it has helped clarify things for me.
What exactly do you mean by "convergence" of the simulations in this context?
Does it have something to do with the calculation of a mean and standard
deviation for delta G, given the multiple snapshots of receptor, ligand, and

Tom Whitington

Quoting Carlos Simmerling <>:

> 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
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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 Sun Sep 11 2005 - 03:53:01 PDT
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