AMBER Archive (2006)

Subject: AMBER: Free energy calculated from mm_pbsa

From: gtg549i_at_mail.gatech.edu
Date: Thu Jul 13 2006 - 02:26:44 CDT

Dear all,

I used mm_pbsa to calculate the free energy of binding for 1000 snapshots after
simulated annealing. When i tried to do the histogram of the energy, i found out
that the gas energy range 0 to -70 kcal/mol. i am wondering if this energy
difference is too large or not. Do i need to do an energy minimization after the
annealing before the mm_pbsa calculation?

Thanks! 

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