AMBER Archive (2006)

Subject: AMBER: MMPBSA entropy question

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Tue Oct 31 2006 - 03:08:55 CST

Hello,

I have several questions about MMPBSA scientific background, maybe trivial,
and especially the for the entropic effect. If I have correctly understood
the method, the solute entropic effect is divided into four parameters :
translation, rotation, vibration and configuration.

In the MMPBSA tutorial I found that the configuration term is "the
configurational entropy contribution from sidechain reorganization. Note that
configurational entropy is neglected in this protocol, but may be
significant." Why only sidechain? If you start with 3 trajectories (ligand,
target and complex) this effect couldn't be overcome?

The translation and rotation terms came directly from statistical mechanics.
Therefore, why these values are only accessible with the normal mode option?

Best regards.
Florent Barbault 

-- 
----------------------------------------------------------
Dr Florent Barbault
Maitre de conferences
Universite Paris VII
Laboratoire ITODYS
1, rue Guy de la Brosse
75005 Paris FRANCE
http://perso.wanadoo.fr/barbault
tel  : (33) 01-44-27-68-21
mail : florent.barbault_at_paris7.jussieu.fr
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