[AMBER] Energy units in mm-pbsa calculations

From: <moitrayee.mbu.iisc.ernet.in>
Date: Tue, 23 Mar 2010 18:27:30 +0530 (IST)

Dear Amber Users,

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 ?
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

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Received on Tue Mar 23 2010 - 07:00:02 PDT
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