Re: [AMBER] Energy units in mm-pbsa calculations

From: Billy Miller III <>
Date: Tue, 23 Mar 2010 09:40:07 -0400

The energy units of GBTOT and PBTOT are in kcal/mol. Your analysis of your
results seem valid. You get different free energies of binding during
different parts of the simulation because the complex is simply not in the
exact same conformation during all of those different time intervals. I
think a more appropriate free energy of binding calculation would include a
long simulation time in order for the calculation to include as many
relevant conformations of the complex as possible. This should give a free
energy of binding that is more agreeable with the true dynamics of the

I hope that helps.

-Bill Miller

On Tue, Mar 23, 2010 at 8:57 AM, <> wrote:

> Dear Amber Users,
> I am doing a stability calculation of a protein using module of
> AMBER9. What are the units of GBTOT and PBTOT. Is it kcal/mol ?
> Also I have performed the calculations over snapshots collected from
> different
> time intervals of the trajectory e.g. 5-7ns, 10-13 ns and 15-17 ns. I get
> different values for GBTOT and PBTOT for each set. However, GBTOT and PBTOT
> within a set are highly convergent. Can this effect arise due to small
> conformation changes within a simulation.
> Looking forward to hear from you.
> Thanks a lot in advance for any help.
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit
> Indian institute of Science
> Bangalore - 560012
> India
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Received on Tue Mar 23 2010 - 07:00:04 PDT
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