Subject: ALA carbonyl flip in alpha helix protein

From: Artem Mamonov <[email-masked]>
Date: Sun, 20 May 2001 17:09:27 -0400

Dear all,
Working on MD simulations (AMBER6, parm96.dat) of a small alpha helix 
protein (gramicidin A) i've noticed that some ALA carbonyls of the 
backbone flip over (~180 degrees) along the helix. I am wondering if it 
can take place in a real life or it's a drawback of the force 
field/parametrisation/methodology. I will appreciate any 
comments/references.

thanks

-- 
Artem Mamonov
Graduate Student
Department Of Chemistry
University Of Pittsburgh
email: [email-masked]