Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA

From: Bill Miller III <>
Date: Sat, 17 Mar 2012 14:19:03 -0400

If the conformation of your two subunits change significantly upon binding
than a single trajectory approach would likely not be as accurate as a
triple trajectory approach (running MD on the complex and both subunits
(receptor and ligand) by themselves. is able to analyze all three
trajectories at once instead of creating those trajectories all from the
same trajectory (single trajectory approach).

I hope that helps.


On Thu, Mar 15, 2012 at 8:18 PM, Wholly Peach <> wrote:

> Dear All,
> For the on-line AMBER advanced tutorial 3 MM-PBSA, it would depend on the
> conformation of the subunit does not change significantly. If the
> conformation of the 2 subunits change significantly after forming the
> complex, then we cannot get the PDB of individua subunits. Then do we have
> some methods for the free binding energy calculation?
> Cheers,
> Wholly
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Mar 17 2012 - 11:30:04 PDT
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