AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA problem

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri Jun 09 2006 - 10:06:34 CDT

Dear Jitrayut

> I am calculating the binding energy of peptide-enzyme with mmpbsa, but
> acctually I am new for mmpbsa so my 2 problems is ,first, how many snapshots
> did I should make ? if my trajectories is 500 ps about 5000 frames
> (0.2pstime step) since the ras-raf tutorial you set to 5 but why ?

The question is not how many snapshots total you should use, but how many
uncorrelated snapshots there are. Writing more snapshots in shorter time
intervalls does not necessarily improve your results the way more
snapshots from a longer trajectory should do. A snapshot every 10 ps was
used in some MM-PBSA studies, but depending on your system you could use
shorter intervalls like 1 ps or less.

> first problem and the second problem is what kind of trajectories used to
> generate the snapshots ? Is it average structure or the entire
> trajectories including heat and equilibrate trajectories ? please help me

You do not want snapshots of an unequilibrated system in your MM-PBSA run
as these would most likely give bad results. Binding free energy is an
equilibrium property so you should get it from an equilibrated structure
with this approach.

Regards,

Thomas
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