AMBER: Amber9: Free Energy

From: <>
Date: Sun, 3 Sep 2006 19:11:44 -0400 (EDT)

Dear Amber users,

I use Amber9 and I would like to determine the (Gibbs) Free Energy
Perturbation (FEP) from cmo5U to U (Uridine). I would like to use the
program “gibbs” to compute this free energy. It seems like the newest
version of Amber (Amber9) does not contain the program gibbs.
Is it possible to integrate this program in Amber9 and use it or could I
use it as a stand alone program? If the answer of one of the above
questions is yes, could anyone guide me through the different steps to be

However, I know that the free energy can be determined with the Sander
module in Amber9. I read the section about thermodynamic integration
method found in the Amber9 manual (page 153 of the hard copy) and since
the numbering of the equations found in the text does not correspond to
the actual numbering of the described equations, I am kind of confused.

I also went trough the tutorial “Thermodynamic integration calculations
using sander” (by Dave Case, Jan 2005). In this tutorial, the three-point
Gaussian integration method is used and yielded a value of 1.75 kcal/mol.
What is the procedure to be followed to carry out the three-point Gaussian

Thank you for your replies!

Dr F. Vendeix

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Received on Wed Sep 06 2006 - 06:07:07 PDT
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