Subject: free energy perturbation with Amber 5

From: meiselba <[email-masked]>
Date: Fri, 13 Dec 2002 11:41:19 +0100

Hello,

I test the Gibbs-Modul from Amber 5.0 with the valine to alanine FEP 
tutorial from the Amber website 
(http://www.amber.ucsf.edu/amber/tutorial/gibbs_box/HTML/xleap_edit_selected.html).
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

Computer-Chemie-Centrum,
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Naegelsbachstraße 25
D-91052 Erlangen