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
India
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 23 2010 - 07:00:02 PDT
