AMBER Archive (2004)

Subject: AMBER: questions on mm_pbsa

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Fri Aug 20 2004 - 07:13:51 CDT

Dear AMBER users,

I have some questions about mm_pbsa approach to calculate binding free
energies.

My first question is about the radii to use to calculate the
electrostatic part of solvation.
It is clear that this choice has a great influence on the results. Is
there any "good choice" ?
For example, when using GB, is it better to use Tsui parameters (igb=1)
or Jayaram ones (igb=4) ?

My second question is about the calculation of vibrationnal entropy with
nmode on AMBER7.
I have a quite big system (two monomers of 218 residues each) and this
is far too much for the
memory of my computers for running nmode. Is there any possibility to
calculate this entropy
without needing too much memory ?

Thanks in advance for all the answers,
Fabien 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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