AMBER Archive (2003)

Subject: 2 questions

From: FyD (fyd_at_u-picardie.fr)
Date: Fri May 09 2003 - 05:02:41 CDT

Dear Amber-Users,
 
I have 2 questions:
 
- If we take the AMBER FF equation, is the hydrophobic interaction between 2 aromatic
residues (for instance) taken into account ? Is it through the vdW term ?
 
- Starting from a wild type fold, I mutated a residue. Using the GBSA strategy, I get a
dE(effective) value of 8 kcal/mol and a dG value of 13 kcal/mol between the mutant and the
wild type protein (1 nanosec productive MD with GB). Can I conclude that the mutation
present a stabilisation or a de-stabilisation effect ? To my opinion, such a dG is too
small...
 
Thanks a lot, regards, Francois