AMBER Archive (2003)

Subject: free energy perturbation (Gibbs/Amber 5)?

From: meiselba (Heike.Meiselbach_at_organik.uni-erlangen.de)
Date: Thu Jan 09 2003 - 10:49:09 CST

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

Heike Meiselbach

Computer-Chemie-Centrum,
Friedrich-Alexander-Universitaet Erlangen-Nuernberg