AMBER Archive (2005)

Subject: AMBER: Request for calculating free energy using AMBER6

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Mon Jun 27 2005 - 06:59:00 CDT

dear amber friends.
 I read a journal written by peter A. Kolman and Teri E. Klein as
COMPUTED FREE ENRGY DIFFRENCES BETWEEN POINT MUTATIONS IN A COLLAGEN
LIKE PEPTIDES, in Biopolymers,58,347-353,2001.
i would like to repeat the free enrgy calcualtion, using the amber6
package in way the above paper mentioned methods.
They calculated the change in free energy between two states, that is
sequence which has glycine replaced by ala. i don't know how to set
the two states as they did. i also like to know in gibbs the 0 states
and 1 states are what? or gibbs calculating free energy or change in
free energy.
i kindly reqest to all please help me in this regard.
thanks 

-- 
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
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