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

From: Ray Luo <>
Date: Wed, 24 Mar 2010 10:48:28 -0700

> 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.
This is normal and that's why you need to make sure your average numbers
are converged.

All the best,

Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: Phones: (949) 824-9528, 9562

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Received on Wed Mar 24 2010 - 11:00:04 PDT
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