free energy perturbation (Gibbs/Amber 5)?

From: meiselba <>
Date: Thu 09 Jan 2003 17:49:09 +0100

Dear all,

Happy new year.
I am currently working on my master thesis which primarily is about free
energy perturbation (FEP) of proteins. In this context I am performing
Molecular Dynamics (MD) with Amber 5.0.

I test the Gibbs-Modul from Amber 5.0 with the valine to alanine FEP
tutorial from the Amber website.
But I don't understand the perturbation charges.
Can you tell me, why the pert.charge in the tutorial for CB is 0.105 and
not the charge for alanine (CB -0.1825)? Why are the other charges not
changed as well?
My last question, what is the actual result (kcal/mol) for this simulation
(valine to alanine)?

Thank you in advance,

Heike Meiselbach

Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Received on Thu Jan 09 2003 - 08:49:09 PST
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