> I am doing a stability calculation of a protein using mm-pbsa.pl module of
> AMBER9. What are the units of GBTOT and PBTOT. Is it kcal/mol ?
Yes.
> 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
==========================================
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: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
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Received on Wed Mar 24 2010 - 11:00:04 PDT
